processtrajectories error

[natlasy]

Very nice work! However I am trying to work with your package and it goes smooth until the step of "processtrajectories" in which I am getting this error:

cellrouter <- processtrajectories(cellrouter, genes2use, path.rank=ranks[3],num.cells = 3, neighs = 1) [1] "parsing trajectory information" Error in complete.cases(paths) : no input has determined the number of cases

Any idea ?

Best, natlasy

[edroaldo]

Thank you and I am sorry you are facing issues. The error message suggest that a previous command, findpaths, did not produce all outpur required. This could be due to your Java version.

Could you please let me know which operation system are you using (Linux/MAC/Windows)? CellRouter does not work on Windows systems. Also, could you please let me know your Java version?

You need to have the Oracle Java installed. In Linux systems, the openJDK is installed by default. https://www.digitalocean.com/community/tutorials/how-to-inst all-java-with-apt-get-on-ubuntu-16-04

You can follow instructions in the following link to set which Java your computer is using: https://askubuntu.com/questions/315646/update-java-alternati ves-vs-update-alternatives-config-java

Also, you may also need to install the following:

install.packages("Vennerable", repos="http://R-Forge.R-project.org")

Please, let me know if that works!

Thanks!

2018-04-23 8:58 GMT-04:00 natlasy notifications@github.com:

Very nice work! However I am trying to work with your package and it goes smooth until the step of "processtrajectories" in which I am getting this error:

cellrouter <- processtrajectories(cellrouter, genes2use, path.rank=ranks[3],num.cells = 3, neighs = 1) [1] "parsing trajectory information" Error in complete.cases(paths) : no input has determined the number of cases

Any idea ?

Best, natlasy

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-- Edroaldo

[natlasy]

Hi edroaldo,

Thanks for your quick reply. I already noticed the issue from other user. But seems that is not my case. I use linux ubuntu 16.4

java version "1.8.0_171" Java(TM) SE Runtime Environment (build 1.8.0_171-b11) Java HotSpot(TM) 64-Bit Server VM (build 25.171-b11, mixed mode)

and I have the library"Vennerable" installed already.

I noticed that when I run the "findpaths" , I get this: getwd() [1] "/mylocation/results"

llrouter <- findpaths(cellrouter, libdir, paste(getwd(), "paths", sep="/"), method="graph") --------------------------: SP_2.SP_1 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 351 New source s added New target t added Network size: 353 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 Number of paths: 230 Number of paths: 240 Number of paths: 250 Number of paths: 260 path size before: 262 path size after: 262 Subnet size: 119 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_2.SP_3 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 351 New source s added New target t added Network size: 353 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 Number of paths: 230 Number of paths: 240 Number of paths: 250 Number of paths: 260 Number of paths: 270 Number of paths: 280 Number of paths: 290 Number of paths: 300 Number of paths: 310 Number of paths: 320 Number of paths: 330 Number of paths: 340 Number of paths: 350 Number of paths: 360 Number of paths: 370 Number of paths: 380 path size before: 380 path size after: 380 Subnet size: 209 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_2.SP_4 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 351 New source s added New target t added Network size: 353 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 Number of paths: 230 Number of paths: 240 Number of paths: 250 Number of paths: 260 Number of paths: 270 Number of paths: 280 Number of paths: 290 path size before: 299 path size after: 299 Subnet size: 193 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_2.SP_5 and so on.

this is the output in each subfolder of the paths;

CellRouter.sh Cells_FlowNetwork_all_paths_subnet.txt Cells_FlowNetwork_scripts.R cell_sources.txt Cells_FlowNetwork_all_paths_subnet_exportGML.R Cells_FlowNetwork_all_paths_totalFlow.txt
Cells_FlowNetwork_scripts.Rout Cells_FlowNetwork_all_paths_subnet.gml
Cells_FlowNetwork_all_paths.txt
cell_sinks.txt

Please let me know if you need any other info.

Best, natlasy

[edroaldo]

Glad to help! The output looks correct. Could you please send me your file Cells_FlowNetwork_scripts.Rout? And also Cells_FlowNetwork_all_paths_subnet.txt? Just want to check a few things.

Thanks!

2018-04-23 9:55 GMT-04:00 natlasy notifications@github.com:

Hi edroaldo,

Thanks for your quick reply. I already noticed the issue from other user. But seems that is not my case. I use linux ubuntu 16.4

java version "1.8.0_171" Java(TM) SE Runtime Environment (build 1.8.0_171-b11) Java HotSpot(TM) 64-Bit Server VM (build 25.171-b11, mixed mode)

and I have the library"Vennerable" installed already.

I noticed that when I run the "findpaths" , I get this: getwd() [1] "/mylocation/results"

llrouter <- findpaths(cellrouter, libdir, paste(getwd(), "paths", sep="/"), method="graph") --------------------------: SP_2.SP_1

1. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 351 New source s added New target t added Network size: 353 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 Number of paths: 230 Number of paths: 240 Number of paths: 250 Number of paths: 260 path size before: 262 path size after: 262 Subnet size: 119 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_2.SP_3
2. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 351 New source s added New target t added Network size: 353 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 Number of paths: 230 Number of paths: 240 Number of paths: 250 Number of paths: 260 Number of paths: 270 Number of paths: 280 Number of paths: 290 Number of paths: 300 Number of paths: 310 Number of paths: 320 Number of paths: 330 Number of paths: 340 Number of paths: 350 Number of paths: 360 Number of paths: 370 Number of paths: 380 path size before: 380 path size after: 380 Subnet size: 209 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_2.SP_4
3. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 351 New source s added New target t added Network size: 353 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 Number of paths: 230 Number of paths: 240 Number of paths: 250 Number of paths: 260 Number of paths: 270 Number of paths: 280 Number of paths: 290 path size before: 299 path size after: 299 Subnet size: 193 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_2.SP_5 and so on.

this is the output in each subfolder of the paths;

CellRouter.sh Cells_FlowNetwork_all_paths_subnet.txt Cells_FlowNetwork_scripts.R cell_sources.txt Cells_FlowNetwork_all_paths_subnet_exportGML.R Cells_FlowNetwork_all_paths_totalFlow.txt Cells_FlowNetwork_scripts.Rout Cells_FlowNetwork_all_paths_subnet.gml Cells_FlowNetwork_all_paths.txt cell_sinks.txt

Please let me know if you need any other info.

Best, natlasy

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-- Edroaldo

[natlasy]

Thanks! Here you are:

R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

[Previously saved workspace restored]

library(gplots);

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

library(ggplot2); library(grid); library(reshape); Warning message: package ‘reshape’ was built under R version 3.4.3 library(reshape2);

Attaching package: ‘reshape2’

The following objects are masked from ‘package:reshape’:

colsplit, melt, recast

Warning message: package ‘reshape2’ was built under R version 3.4.3

library(plyr);

Attaching package: ‘plyr’

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rename, round_any

library(RColorBrewer); library(igraph);

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

decompose, spectrum

The following object is masked from ‘package:base’:

union

Warning message: package ‘igraph’ was built under R version 3.4.3

library(Vennerable); Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

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normalize, union

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IQR, mad, sd, var, xtabs

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anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Attaching package: ‘graph’

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Loading required package: RBGL

Attaching package: ‘RBGL’

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Loading required package: lattice Loading required package: gtools

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Loading required package: xtable Warning messages: 1: package ‘Vennerable’ was built under R version 3.4.3 2: package ‘graph’ was built under R version 3.4.3 3: package ‘RBGL’ was built under R version 3.4.3

subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

--------------------------------------------------------------------------

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

--------------------------------------------------------------------------

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

--------------------------------------------------------------------------

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

--------------------------------------------------------------------------

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood(graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

--------------------------------------------------------------------------

proc.time() user system elapsed 3.236 0.112 3.345

and the other file the head:

from to edge_flow Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 t 8.034522962803681 JCD5.Pl1.15074.unpaired_uniq.NoUMIdups.ATGCGACG.Cell.58 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.5625 JCD8.Pl1.15071.unpaired_uniq.NoUMIdups.AGTTGTGT.Cell.46 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.470588235294118 JCD9.Pl1.15012.unpaired_uniq.NoUMIdups.TTCAGCGT.Cell.224 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.388888888888889 Healthy.JCD7.Pl1.15021.unpaired_uniq.NoUMIdups.TCTGTGAG.Cell.199 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.21106792296857507

Best, natlasy

[natlasy]

Now I realized: Warning messages: 1: package ‘Vennerable’ was built under R version 3.4.3 2: package ‘graph’ was built under R version 3.4.3 3: package ‘RBGL’ was built under R version 3.4.3

and my R version is 3.4.1 ..

Not sure if this has the impact on the workflow....

Cheers, natlasy

[edroaldo]

Everything looks just fine. That's interesting. Would you mind to send me your script, so I can check line by line what your are doing? I think a directory might be set incorrectly. Is there a folder "paths" inside your folder "results"? Were you able to run any of the tutorials?

Thanks!

2018-04-23 10:08 GMT-04:00 natlasy notifications@github.com:

Thanks! Here you are:

R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

[Previously saved workspace restored]

library(gplots);

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

library(ggplot2); library(grid); library(reshape); Warning message: package ‘reshape’ was built under R version 3.4.3 library(reshape2);

Attaching package: ‘reshape2’

The following objects are masked from ‘package:reshape’:

colsplit, melt, recast

Warning message: package ‘reshape2’ was built under R version 3.4.3

library(plyr);

Attaching package: ‘plyr’

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rename, round_any

library(RColorBrewer); library(igraph);

Attaching package: ‘igraph’

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Warning message: package ‘igraph’ was built under R version 3.4.3

library(Vennerable); Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

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clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

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normalize, union

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IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Attaching package: ‘graph’

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degree, edges, intersection

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join

Loading required package: RBGL

Attaching package: ‘RBGL’

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Loading required package: lattice Loading required package: gtools

Attaching package: ‘gtools’

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Loading required package: xtable Warning messages: 1: package ‘Vennerable’ was built under R version 3.4.3 2: package ‘graph’ was built under R version 3.4.3 3: package ‘RBGL’ was built under R version 3.4.3

subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

-----------------------------------------------------------

---

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

-----------------------------------------------------------

---

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

-----------------------------------------------------------

---

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

-----------------------------------------------------------

---

library(gplots); library(ggplot2); library(grid); library(reshape); library(reshape2); library(plyr); library(RColorBrewer); library(igraph); library(Vennerable); subnet <- read.table('Cells_FlowNetwork_all_paths_subnet.txt', sep=' ', header = TRUE); totalFlow <- read.table('Cells_FlowNetwork_all_paths_totalFlow.txt', sep=' ', header = TRUE); colnames(subnet) <- c('from', 'to', 'weight'); iG <- graph.data.frame(subnet, directed=FALSE); V(iG)$label <- V(iG)$name; V(iG)[as.vector(totalFlow$cell)]$totalFlows <- totalFlow$flows; V(iG)$degree <- igraph::degree(iG); neighS <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='s'))))$name; neighT <- V(induced.subgraph(graph=iG,vids=unlist(neighborhood( graph=iG,order=1,nodes='t'))))$name; V(iG)$props = rep("INTER", length(V(iG)$name)); V(iG)[match(neighS, V(iG)$name)]$props = "SOURCE"; V(iG)[match(neighT, V(iG)$name)]$props = "TARGET"; iG2 <- delete.vertices(iG, c('s','t')); write.graph(iG2,'Cells_FlowNetwork_all_paths_subnet.gml', format = 'gml');

-----------------------------------------------------------

---

proc.time() user system elapsed 3.236 0.112 3.345

and the other file the head:

from to edge_flow Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 t 8.034522962803681 JCD5.Pl1.15074.unpaired_uniq.NoUMIdups.ATGCGACG.Cell.58 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.5625 JCD8.Pl1.15071.unpaired_uniq.NoUMIdups.AGTTGTGT.Cell.46 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.470588235294118 JCD9.Pl1.15012.unpaired_uniq.NoUMIdups.TTCAGCGT.Cell.224 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.388888888888889 Healthy.JCD7.Pl1.15021.unpaired_uniq.NoUMIdups.TCTGTGAG.Cell.199 Healthy.JCD6.Pl1.15069.unpaired_uniq.NoUMIdups.CGTCGTTT.Cell.377 0.21106792296857507

Best, natlasy

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-- Edroaldo

[edroaldo]

It should not impact the workflow. I tested this with previous R versions at the beginning...

Thanks!

2018-04-23 10:16 GMT-04:00 natlasy notifications@github.com:

Now I realized: Warning messages: 1: package ‘Vennerable’ was built under R version 3.4.3 2: package ‘graph’ was built under R version 3.4.3 3: package ‘RBGL’ was built under R version 3.4.3

and my R version is 3.4.1 ..

Not sure if this has the impact on the workflow....

Cheers, natlasy

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-- Edroaldo

[natlasy]

library("Vennerable") source("/mylocation/scRNA/cellrouter-master/CellRouter_Class.R") libdir <- "/mylocation/scRNA/cellrouter-master/CellRouter/"

getwd() [1] "/mylocation/results"

ndata <- tab genes <- sapply(strsplit(rownames(ndata), split=":", fixed=TRUE), function(x){x[2]}) map <- data.frame(id=rownames(ndata), symbol=genes, stringsAsFactors = FALSE) ndata <- averageIds(ndata, map, "symbol")

ndata[1:3,1:3] JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGGAGCA.Cell.204 DPM1 0 SCYL3 0 C1orf112 0 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGTGGCT.Cell.24 DPM1 0 SCYL3 0 C1orf112 0 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.ACACCGTG.Cell.41 DPM1 0 SCYL3 0 C1orf112 0

var <- apply(ndata, 1, var) var <- var[which(var > 0)] ndata <- ndata[names(var),]

pca <- prcomp(t(ndata), scale=TRUE, center=TRUE) loadings <- pca$rotation num_pc <- 5 quantile <- 0.975 genes2use <- unique(as.vector(unlist(apply(loadings[,1:num_pc], 2, function(x){names(x[which(abs(x) >= quantile(x, quantile))])}))))

head(genes2use) [1] "GAS7" "UFL1" "WWTR1" "GLRX2" "FAS" "B4GALT7"

cellrouter <- CellRouter(expdata=ndata, annotations=colnames(ndata))

matrix <- read.table("/mylocation/tsne.table") colnames(matrix) <- c("tSNE1", "tSNE2") cellrouter@rdimension <- matrix

head(matrix) tSNE1 tSNE2 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGGAGCA.Cell.204 -13.59337 4.648100 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGTGGCT.Cell.24 -13.73863 10.940450

cellrouter <- findsubpopulations(cellrouter, 5, "jaccard", "kNN_network.gml") cellrouter <- diffexpr(cellrouter, column="population", pvalue = 0.05) markers <- findmarkers(cellrouter) plotReducedDimension(cellrouter, 3.5, 3.5, filename="tSNE.cellrout.pdf")

cellrouter <- createKNN(cellrouter, 10, "jaccard", "kNN_network_trajectory.gml") filename <- "cell_edge_weighted_network.txt" write.table(cellrouter@graph$edges, file=filename, sep="\t", row.names=FALSE, col.names = FALSE, quote=FALSE) #input network

sources <- c("SP_2") targets <- setdiff(as.vector(cellrouter@sampTab$population), sources) methods <- c("euclidean", "maximum", "manhattan","canberra","binary", "graph") llrouter <- findpaths(cellrouter, libdir, paste(getwd(), "paths", sep="/"), method="graph") save(cellrouter, file="CellRouter_StemID.R")

here I had to cp the "cell_edge_weighted_network.txt" file from 'results' directory to 'paths' directory as it was mentioned in "NET=/mylocation/results/paths/cell_edge_weighted_network.txt" from bash -x CellRouter.sh

cellrouter <- get(load("CellRouter_StemID.R")) ranks <- c("path_cost", "path_flow", "rank", "length") cellrouter <- processtrajectories(cellrouter, genes2use, path.rank=ranks[3],num.cells = 3, neighs = 1)

getwd() [1] "/mylocation/results"

Thanks! natlasy

[edroaldo]

Everything looks fine. Were you able to reproduce the examples in the website? If you do: filename <- "paths/cell_edge_weighted_network.txt"

instead of filename <- "cell_edge_weighted_network.txt" in filename <- "cell_edge_weighted_network.txt" write.table(cellrouter@graph$edges, file=filename, sep="\t", row.names=FALSE, col.names = FALSE, quote=FALSE) #input network

you do not need to cp cell_edge_weighted_network.txt to the paths directory. Actually, I think this is the source of your problem. The findpaths function will save the directory "paths/"each_transition" as part of the CellRouter object, pointing to each gml file in each folder inside the "paths" folder. Simply copying the cell_edge_weighted_network.txt to paths will not help because CellRouter is expecting to find the "each_transition" sub-folders inside results.

To check that, could you please double-check if this variable points to the right location? cellrouter@directory Please, send me the list of directories in cellrouter@directory

This should be: "/mylocation/results/paths/". Probably, you have only "/mylocation/results"

Please, let me know this info. I think this could be the problem.

Thanks!

2018-04-23 10:29 GMT-04:00 natlasy notifications@github.com:

library("Vennerable") source("/mylocation/scRNA/cellrouter-master/CellRouter_Class.R") libdir <- "/mylocation/scRNA/cellrouter-master/CellRouter/"

getwd() [1] "/mylocation/results"

ndata <- tab genes <- sapply(strsplit(rownames(ndata), split=":", fixed=TRUE), function(x){x[2]}) map <- data.frame(id=rownames(ndata), symbol=genes, stringsAsFactors = FALSE) ndata <- averageIds(ndata, map, "symbol")

ndata[1:3,1:3] JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGGAGCA.Cell.204 DPM1 0 SCYL3 0 C1orf112 0 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGTGGCT.Cell.24 DPM1 0 SCYL3 0 C1orf112 0 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.ACACCGTG.Cell.41 DPM1 0 SCYL3 0 C1orf112 0

var <- apply(ndata, 1, var) var <- var[which(var > 0)] ndata <- ndata[names(var),]

pca <- prcomp(t(ndata), scale=TRUE, center=TRUE) loadings <- pca$rotation num_pc <- 5 quantile <- 0.975 genes2use <- unique(as.vector(unlist(apply(loadings[,1:num_pc], 2, function(x){names(x[which(abs(x) >= quantile(x, quantile))])}))))

head(genes2use) [1] "GAS7" "UFL1" "WWTR1" "GLRX2" "FAS" "B4GALT7"

cellrouter <- CellRouter(expdata=ndata, annotations=colnames(ndata))

matrix <- read.table("/mylocation/tsne.table") colnames(matrix) <- c("tSNE1", "tSNE2") cellrouter@rdimension <- matrix

head(matrix) tSNE1 tSNE2 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGGAGCA.Cell.204 -13.59337 4.648100 JCD10.Pl1.15022.unpaired_uniq.NoUMIdups.AAGTGGCT.Cell.24 -13.73863 10.940450

cellrouter <- findsubpopulations(cellrouter, 5, "jaccard", "kNN_network.gml") cellrouter <- diffexpr(cellrouter, column="population", pvalue = 0.05) markers <- findmarkers(cellrouter) plotReducedDimension(cellrouter, 3.5, 3.5, filename="tSNE.cellrout.pdf")

cellrouter <- createKNN(cellrouter, 10, "jaccard", "kNN_network_trajectory.gml") filename <- "cell_edge_weighted_network.txt" write.table(cellrouter@graph$edges, file=filename, sep="\t", row.names=FALSE, col.names = FALSE, quote=FALSE) #input network

sources <- c("SP_2") targets <- setdiff(as.vector(cellrouter@sampTab$population), sources) methods <- c("euclidean", "maximum", "manhattan","canberra","binary", "graph") llrouter <- findpaths(cellrouter, libdir, paste(getwd(), "paths", sep="/"), method="graph") save(cellrouter, file="CellRouter_StemID.R") here I had to cp the "cell_edge_weighted_network.txt" file from 'results' directory to 'paths' directory as it was mentioned in "NET=/mylocation/results/paths/cell_edge_weighted_network.txt" from bash -x CellRouter.sh

cellrouter <- get(load("CellRouter_StemID.R")) ranks <- c("path_cost", "path_flow", "rank", "length") cellrouter <- processtrajectories(cellrouter, genes2use, path.rank=ranks[3],num.cells = 3, neighs = 1)

getwd() [1] "/mylocation/results"

Thanks! natlasy

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-- Edroaldo

[natlasy]

I tried adding 'path/' to filename and I got the same error.Below is what I get from the directory:

cellrouter@directory list()

Thanks! natlasy

[natlasy]

I noticed I am getting the below warning in between, not sue if this is the problem

cellrouter <- createKNN(cellrouter, 10, "jaccard", "kNN_network_trajectory.gml") [1] "updating CellRouter object" Warning message: In write.graph.gml(graph, file, ...) : At foreign.c:2616 :A boolean graph attribute was converted to numeric

Thanks!

[natlasy]

All right, I now realized that basically, after installation of all the dependencies and etc for CellRouter, my R environment has been changed and it is just screwed; I no longer able to run the other packages that I use to work with. Meaning I have to deal with building/fixing my R again :(

[edroaldo]

This is why you are getting an errors with processtrajectories. I need to know if you created a folder named paths inside your folder results. You should have a list of directories in cellrouter@directory

I also need to know if you were able to run the first tutorial in the github website. I have never seen the issue your are facing. Thanks!

On Tue, Apr 24, 2018, 4:43 AM natlasy notifications@github.com wrote:

I tried adding 'path/' to filename and I got the same error.Below is what I get from the directory:

cellrouter@directory list()

Thanks! natlasy

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[edroaldo]

This is an issue...

On Tue, Apr 24, 2018, 4:45 AM natlasy notifications@github.com wrote:

I noticed I am getting the below warning in between, not sue if this is the problem

cellrouter <- createKNN(cellrouter, 10, "jaccard", "kNN_network_trajectory.gml") [1] "updating CellRouter object" Warning message: In write.graph.gml(graph, file, ...) : At foreign.c:2616 :A boolean graph attribute was converted to numeric

Thanks!

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[edroaldo]

I am sorry you are having troubles but is unusual to see that installation of new packages your R installation. Have you tried to restart R studio? Thanks!

On Tue, Apr 24, 2018, 5:39 AM natlasy notifications@github.com wrote:

All right, I now realized that basically, after installation of all the dependencies and etc for CellRouter, my R environment has been changed and it is just screwed; I no longer able to run the other packages that I use to work with. Meaning I have to deal with building/fixing my R again :(

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[natlasy]

Hi edroaldo,

I had to re-build my R again. Anyway, I started from scratch, build to latest R 3.4.4 and installed all the dependent packages. I have my java set to oracle and I ran this time one of the examples provided in the CellRouter package. Everything again went fine and all the plots are reproducible but when I run the "processtrajectories" step I am getting the same error:

cellrouter <- processtrajectories(cellrouter, genes2use, path.rank=ranks[3],num.cells = 3, neighs = 1) [1] "parsing trajectory information" Error in complete.cases(paths) : no input has determined the number of cases cellrouter@directory list()

I am working from 'mylocation/resuts' directory ( getwd() ) and I have 'paths' directory in my 'mylocation/results' diroctory.

Any idea !?

Thanks

[edroaldo]

Your problem is happening before that. It is very weird to the cellroutet@directory empty. Is there any error in your findpaths function? Can I see how you are calling the findpaths function? If you send me your script until the processtrajectory function again would be helpful. Thanks!

On Wed, Apr 25, 2018, 6:13 AM natlasy notifications@github.com wrote:

Hi edroaldo,

I had to re-build my R again. Anyway, I started from scratch, build to latest R 3.4.4 and installed all the dependent packages. I have my java set to oracle and I ran this time one of the examples provided in the CellRouter package. Everything again went fine and all the plots are reproducible but when I run the "processtrajectories" step I am getting the same error:

cellrouter <- processtrajectories(cellrouter, genes2use, path.rank=ranks[3],num.cells = 3, neighs = 1) [1] "parsing trajectory information" Error in complete.cases(paths) : no input has determined the number of cases cellrouter@directory list()

I am working from 'mylocation/resuts' directory ( getwd() ) and I have 'paths' directory in my 'mylocation/results' diroctory.

Any idea !?

Thanks

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[natlasy]

I'm getting this warning from 'findpath' and also from 'findsubpopulations' function:

cellrouter <- createKNN(cellrouter, 10, "jaccard", "kNN_network_trajectory.gml") [1] "updating CellRouter object" Warning message: In write.graph.gml(graph, file, ...) : At foreign.c:2616 :A boolean graph attribute was converted to numeric

Thanks!

[natlasy]

sorry, that warning is not coming from 'findpath' function. Here is my 'findpath' output:

llrouter <- findpaths(cellrouter, libdir, paste(getwd(), "paths", sep="/"), method="graph") --------------------------: SP_20.SP_1 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 path size before: 162 path size after: 162 Subnet size: 145 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_2 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_3 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 path size before: 154 path size after: 154 Subnet size: 108 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_4 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 path size before: 126 path size after: 126 Subnet size: 98 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_5 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 188 path size after: 188 Subnet size: 153 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_6 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 path size before: 173 path size after: 173 Subnet size: 197 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_7 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 path size before: 103 path size after: 103 Subnet size: 94 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_8 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 path size before: 148 path size after: 148 Subnet size: 149 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_9 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_10 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 180 path size after: 180 Subnet size: 189 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_11 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 path size before: 134 path size after: 134 Subnet size: 143 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_12 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 path size before: 133 path size after: 133 Subnet size: 142 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_13 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_14 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 path size before: 96 path size after: 96 Subnet size: 103 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_15 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 path size before: 164 path size after: 164 Subnet size: 150 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_16 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 189 path size after: 189 Subnet size: 144 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_17 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 path size before: 112 path size after: 112 Subnet size: 116 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_18 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 8 path size after: 8 Subnet size: 69 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_19 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 path size before: 158 path size after: 158 Subnet size: 122 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_21 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 path size before: 154 path size after: 154 Subnet size: 99 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_22 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 186 path size after: 186 Subnet size: 132 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_23 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 path size before: 220 path size after: 220 Subnet size: 144 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_24 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 path size before: 161 path size after: 161 Subnet size: 130 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R

[edroaldo]

The warning msgs are fine. They do not affect anything.

I have no idea what it is going on. It does not make any sense the findpaths function finish with no errors and cellrouter@directory being empty. If findpaths is suceffuly completed, cellrouter@directory has to contain a list of directories.

Are the subfolders created inside the paths folder? Like, does the directory SP_20.SP_24 exists? Sorry for the many questions,

If the findpaths function worked, the subfolders are created, and there is no directory in cellrouter@directory, this does not make sense...

I usually run CellRouter from 'mylocation' and not 'mylocation/results'. It should not affect anything unless other directoryies are not set correctly. Could you please try to run from 'mylocation' and update your script like this, and let me know the results?:

cellrouter <- createKNN(cellrouter, 10, 'jaccard', 'results/paths/kNN_network_trajectory.gml') filename <- "results/paths/cell_edge_weighted_network.txt" write.table(cellrouter@graph$edges, file=filename, sep='\t', row.names=FALSE, col.names = FALSE, quote=FALSE) #input network

select starting subpopulation

sources <- c('SP_20')

all other subpopulations are targets

targets <- setdiff(as.vector(cellrouter@sampTab$population), sources) methods <- c("euclidean", "maximum", "manhattan","canberra","binary", 'graph') #graph for distances in KNN cellrouter <- findpaths(cellrouter, libdir, paste(getwd(), 'results/paths', sep='/'), method="graph")

Thanks for your patience!

2018-04-25 7:45 GMT-04:00 natlasy notifications@github.com:

sorry, that warning is not coming from 'findpath' function. Here is my 'findpath' output:

llrouter <- findpaths(cellrouter, libdir, paste(getwd(), "paths", sep="/"), method="graph") --------------------------: SP_20.SP_1

1. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 path size before: 162 path size after: 162 Subnet size: 145 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_2
2. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_3
3. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 path size before: 154 path size after: 154 Subnet size: 108 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_4
4. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 path size before: 126 path size after: 126 Subnet size: 98 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_5
5. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 188 path size after: 188 Subnet size: 153 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_6
6. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 path size before: 173 path size after: 173 Subnet size: 197 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_7
7. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 path size before: 103 path size after: 103 Subnet size: 94 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_8
8. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 path size before: 148 path size after: 148 Subnet size: 149 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_9
9. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_10
10. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 180 path size after: 180 Subnet size: 189 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_11
11. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 path size before: 134 path size after: 134 Subnet size: 143 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_12
12. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 path size before: 133 path size after: 133 Subnet size: 142 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_13
13. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_14
14. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 path size before: 96 path size after: 96 Subnet size: 103 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_15 https://maps.google.com/?q=SP_20.SP_15&entry=gmail&source=g
15. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 path size before: 164 path size after: 164 Subnet size: 150 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_16
16. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 189 path size after: 189 Subnet size: 144 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_17
17. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 path size before: 112 path size after: 112 Subnet size: 116 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_18
18. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow path size before: 8 path size after: 8 Subnet size: 69 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_19
19. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 path size before: 158 path size after: 158 Subnet size: 122 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_21
20. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 path size before: 154 path size after: 154 Subnet size: 99 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_22
21. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 path size before: 186 path size after: 186 Subnet size: 132 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_23
22. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 Number of paths: 170 Number of paths: 180 Number of paths: 190 Number of paths: 200 Number of paths: 210 Number of paths: 220 path size before: 220 path size after: 220 Subnet size: 144 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R --------------------------: SP_20.SP_24
23. Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1007 New source s added New target t added Network size: 1009 Computing flow Number of paths: 10 Number of paths: 20 Number of paths: 30 Number of paths: 40 Number of paths: 50 Number of paths: 60 Number of paths: 70 Number of paths: 80 Number of paths: 90 Number of paths: 100 Number of paths: 110 Number of paths: 120 Number of paths: 130 Number of paths: 140 Number of paths: 150 Number of paths: 160 path size before: 161 path size after: 161 Subnet size: 130 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R

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[natlasy]

Dear edroaldo,

I'm so sorry!! I found the problem which is really silly... There was a typo error in the 'findpath' function which was set to 'llrouter' instead of 'cellrouter' ! that's why the paths were not be able to looked in... My bad... sorry for this and thanks a lot for your follow up and help !

Best, natlasy

[edroaldo]

No problem at all! Glad that it worked and please let me k2ow if you need anything else. Thanks!

On Thu, Apr 26, 2018, 5:07 AM natlasy notifications@github.com wrote:

Dear edroaldo,

I'm so sorry!! I found the problem which is really silly... There was a typo error in the 'findpath' function which was set to 'llrouter' instead of 'cellrouter' ! that's why the paths were not be able to looked in... My bad... sorry for this and thanks a lot for your follow up and help !

Best, natlasy

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[edroaldo]

You need to increase the parameter k in the function buildKNN to have a connected graph. When you use the plotKNN function, do you see connections between your cluster or just intracluster connections? If you do not see connections between clusters, try to increase the parameter k accordingly.

Thanks!

On Fri, Aug 3, 2018, 8:56 AM fereshtehizadi notifications@github.com wrote:

Excuse me, I also faced this problem when working with more cell

cellrouter <- findPaths(cellrouter, column='res.1', libdir, paste(getwd(), 'results/paths', sep='/'), method="graph") -------------------Transition: 9.2 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.3 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.0 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.7 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.5 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.1 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.8 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.4 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R -------------------Transition: 9.6 ----------------------- 1) Computing flow network Creating flow network... Number of sources: 1 Number of sinks: 1 Network size before: 1641 New source s added New target t added Network size: 1643 Computing flow path size before: 0 path size after: 0 Subnet size: 0 merging: Cells_FlowNetwork_all_paths_subnet_exportGML.R library(igraph) ranks <- c('path_cost', 'path_flow', 'rank', 'length') cellrouter <- processTrajectories(cellrouter, rownames(cellrouter@ndata), path.rank=ranks[3], num.cells = 3, neighs = 3,column.ann = 'res.1', column.color = 'res.1_color') [1] "parsing trajectory information" Show Traceback

Rerun with Debug Error in complete.cases(paths) : no input has determined the number of cases

cellrouter@sampTab[1:5,] sample_id nGene nUMI conditions res.1 res.1_color population colors community s0.1 s0.1 8262 2711166 s0.1 9 #FF7F00 1 #FF7F00 1 s0.2 s0.2 7423 2263317 s0.2 9 #FF7F00 1 #FF7F00 1 s0.3 s0.3 8104 2536867 s0.3 9 #FF7F00 1 #FF7F00 1 s0.4 s0.4 8588 2635184 s0.4 9 #FF7F00 1 #FF7F00 1 s0.5 s0.5 8004 2909114 s0.5 9 #FF7F00 1 #FF7F00 1

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