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edroaldo / cellrouter

Reconstruction of complex single-cell trajectories using CellRouter
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Using seurat for cellrouter trajectory analysis #13

Open fereshtehizadi opened 6 years ago

fereshtehizadi commented 6 years ago

Hi,

I have already my cell clustered by seurat, now I want to use cell router for trajectory analysis? how that would be please? saying cellrouter@sampTab will help but I don't know how to use that for using my seurat clusters here

Thanks a lot for any help

fereshtehizadi commented 6 years ago

Sorry but I have tried many many times

> libdir='/Users/dicty/Downloads/fereshteh/CellRouter'
> cellrouter <- findPaths(cellrouter, column='seuratClusters', libdir, paste(getwd(), 'results/paths/', sep='/'), method="graph")
1) Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
1) Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
> libdir="/Users/dicty/Downloads/fereshteh/CellRouter"
> cellrouter <- findPaths(cellrouter, column='seuratClusters', libdir, paste(getwd(), 'results/paths/', sep='/'), method="graph")
1) Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
1) Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
> libdir="/Users/dicty/Downloads/fereshteh/CellRouter/"
> 
> cellrouter <- findPaths(cellrouter, column='seuratClusters', libdir, paste(getwd(), 'results/paths/', sep='/'), method="graph")
1) Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
1) Computing flow network
Error: Could not find or load main class cellrouter.CellRouter
Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter
>

inside the CellRouter folder I have commons-cli-1.2-javadoc.jar , commons-cli-1.2-sources.jar, commons-cli-1.2.jar, JRI.jar, JRIEngine.jar and REngine.jar

edroaldo commented 6 years ago

You should keep the cellrouter folder as in the github website... not sure if it will work if you put all jar files into a single folder. Just keep the CellRouter folder from github as it is and see libdir accordingly. This should not be so difficult to run unless you are changing things in a way that I am not aware of...

On Tue, Jul 31, 2018, 2:38 PM fereshtehizadi notifications@github.com wrote:

Sorry but I have tried many many times

libdir='/Users/dicty/Downloads/fereshteh/CellRouter' cellrouter <- findPaths(cellrouter, column='seuratClusters', libdir, paste(getwd(), 'results/paths/', sep='/'), method="graph") 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter libdir="/Users/dicty/Downloads/fereshteh/CellRouter" cellrouter <- findPaths(cellrouter, column='seuratClusters', libdir, paste(getwd(), 'results/paths/', sep='/'), method="graph") 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter libdir="/Users/dicty/Downloads/fereshteh/CellRouter/"

cellrouter <- findPaths(cellrouter, column='seuratClusters', libdir, paste(getwd(), 'results/paths/', sep='/'), method="graph") 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter 1) Computing flow network Error: Could not find or load main class cellrouter.CellRouter Caused by: java.lang.ClassNotFoundException: cellrouter.CellRouter

inside the CellRouter folder I have commons-cli-1.2-javadoc.jar , commons-cli-1.2-sources.jar, commons-cli-1.2.jar, JRI.jar, JRIEngine.jar and REngine.jar

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fereshtehizadi commented 6 years ago

Excuse me, I did not understand you well. Don't you mean that I should download jar files one by one and put them all 6 jar files in a folder named CellRouter?? :( :(

edroaldo commented 6 years ago

No, I meant to download the Cellrouter folder from github and set libdir accordingly... please try that... it should work....

On Tue, Jul 31, 2018, 2:49 PM fereshtehizadi notifications@github.com wrote:

Excuse me, I did not understand you well. Don't you mean that I should download jar files one by one and put them all 6 jar files in a folder named CellRouter?? :( :(

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fereshtehizadi commented 6 years ago

Excuse me, how to download that? by right clicking on the folder I can only download CellRouter.html

edroaldo commented 6 years ago

Clone the github repository again and then copy the folder to a location of your preference. Then set libdir accordingly...

On Tue, Jul 31, 2018, 2:53 PM fereshtehizadi notifications@github.com wrote:

Excuse me, how to download that? by right clicking on the folder I can only download CellRouter.html

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fereshtehizadi commented 6 years ago

Thank you worked finally and now I am waiting to cellrouter <- clusterGenesPseudotime(cellrouter, 5) task be finished

I have never seen such a patient and kind person in scientific forums

Thanks a lot once more for all of your precious efforts in helping me

edroaldo commented 6 years ago

Fantastic! I am very glad to help! I am sorry for the trouble btw. Good thing is that it finally worked!

Let me know if you have further issues/questions. I might be slower to reply from now on...

Thanks much!

On Tue, Jul 31, 2018, 3:12 PM fereshtehizadi notifications@github.com wrote:

Thank you worked finally and now I am waiting to cellrouter <- clusterGenesPseudotime(cellrouter, 5) task be finished

I have never seen such a patient and kind person in scientific forums

Thanks a lot once more for all of your precious efforts in helping me

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fereshtehizadi commented 6 years ago

Thank you,

Actually I am finishing the tutorial 


> 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 = 'seuratClusters', column.color = 'seuratClusters_color')
> 
> names <- unique(names(cellrouter@pathsinfo$distr))
> cellrouter <- correlationPseudotime(cellrouter, type='spearman')
> cellrouter <- topGenes(cellrouter, 0.8, 0.1)
> 
> 
> cellrouter <- smoothDynamics(cellrouter, names)

> 

> 

> 

> 

> cellrouter <- clusterGenesPseudotime(cellrouter, 3)

> save(cellrouter, file='results/CellRouter_Processed.R')
> grn.data <- buildGRN(cellrouter, species = 'Mm', genes.use = rownames(cellrouter@ndata), zscore = 5, filename = 'results/GRN.R')
> plotClusterHeatmap(cellrouter, names, 10, 10, 2, 'results/dynamics.pdf')
 Show Traceback

 Rerun with Debug
 Error in unit(rep_len(1, nrow), "null") : 
  'x' and 'units' must have length > 0 In addition: Warning message:
In matrix(seq(1, cols * ceiling(numPlots/cols)), ncol = cols, nrow = ceiling(numPlots/cols)) :
  data length exceeds size of matrix
edroaldo commented 6 years ago

Can you show me the content of names? You can try to select trajectory like 0.3 for the trajectory from cluster 0 to 3 for example....

Thanks!

On Jul 31, 2018 3:22 PM, "fereshtehizadi" notifications@github.com wrote:

Thank you,

Actually I am finishing the tutorial

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 = 'seuratClusters', column.color = 'seuratClusters_color')

names <- unique(names(cellrouter@pathsinfo$distr)) cellrouter <- correlationPseudotime(cellrouter, type='spearman') cellrouter <- topGenes(cellrouter, 0.8, 0.1)

cellrouter <- smoothDynamics(cellrouter, names)

cellrouter <- clusterGenesPseudotime(cellrouter, 3)

save(cellrouter, file='results/CellRouter_Processed.R') grn.data <- buildGRN(cellrouter, species = 'Mm', genes.use = rownames(cellrouter@ndata), zscore = 5, filename = 'results/GRN.R') plotClusterHeatmap(cellrouter, names, 10, 10, 2, 'results/dynamics.pdf') Show Traceback

Rerun with Debug Error in unit(rep_len(1, nrow), "null") : 'x' and 'units' must have length > 0

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fereshtehizadi commented 6 years ago

Thanks a lot names is 0.1 and 0.2


> cellrouter <- topGenes(cellrouter, 0.8, 0.1)
> cellrouter <- smoothDynamics(cellrouter, names)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> cellrouter <- clusterGenesPseudotime(cellrouter, 3)
> grn.data <- buildGRN(cellrouter, species = 'Mm', genes.use = rownames(cellrouter@ndata), zscore = 5, filename = 'results/GRN.R')
> 
> plotClusterHeatmap(cellrouter, names, 10, 10, 2, 'results/dynamics.pdf')
> 
> plotClusters(cellrouter, names[2], 2, 400, 450, 'results/cluster_dynamics.png')
> 
> transitions <- c('0.1','0.2') #transitions to be analyzed
> 
> transitions <- c('0.1','0.2')
> grn.scores <- grnscores(cellrouter, ggrn = grn.data$GRN, tfs = grn.data$tfs, transitions = transitions, direction='both', flip=TRUE, q.up=0.75, q.down=0.25,
+                         dir.targets='up', columns=2, width=5, height=7, filename='results/GRN_scores')
Warning messages:
1: In min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
2: In max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
3: In min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
4: In max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
> plottr(cellrouter, p, grn.scores[[p]]$scores, cluster=FALSE, 2, 4.5, 5.5, paste('results/', p, 'Regulators_6.2_transition.pdf',sep=''))
 Show Traceback

 Rerun with Debug
 Error in names(x) <- value : 
  'names' attribute [500] must be the same length as the vector [0]
edroaldo commented 6 years ago

Which species? Is your data mouse data?

On Wed, Aug 1, 2018, 5:52 AM fereshtehizadi notifications@github.com wrote:

Thanks a lot names is 0.1 and 0.2

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fereshtehizadi commented 6 years ago

Sorry, I am working with Dictyostelium discoideum for example _DDBG0267412 is a marker gene in this organism of Spore stage in development

edroaldo commented 6 years ago

Old. So you need to cha ge 'Mm' in the buildGRN function to reflect your organism. Mm is for mouse, Hs for human and I do not know for your species. You might need to install additional packages on this case.... Thanks!

On Wed, Aug 1, 2018, 8:58 AM fereshtehizadi notifications@github.com wrote:

Sorry, I am working with Dictyostelium discoideum for example DDB_G0267412 is a marker gene in this organism of Spore stage in development

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fereshtehizadi commented 6 years ago

Thank you, what package is being used in cell router for human and mouse? so perhaps a similar package exists for Dictyostelium discoideum

edroaldo commented 6 years ago

GO.db, org.Mm.xx and org.Hs.xx I do not remember by heart...

On Wed, Aug 1, 2018, 9:24 AM fereshtehizadi notifications@github.com wrote:

Thank you, what package is being used in cell router for human and mouse so perhaps a similar package exists for Dictyostelium discoideum

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fereshtehizadi commented 6 years ago

Thank you, likely there is no such a package in Bioconductor for this organism but there is something like MeSH.Ddi.AX4.eg.db

I don't want to give up

edroaldo commented 6 years ago

Weird. I think it should be a package. You can give up the GRN analysis but others should be fine....

On Wed, Aug 1, 2018, 9:40 AM fereshtehizadi notifications@github.com wrote:

Thank you, likely there is no such a package in bioconductor for this organism

So I should give up?

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fereshtehizadi commented 6 years ago

Sorry, there are some zip files for GO and annotation for my organism in http://dictybase.org/Downloads/, Also somethings in dicty biomart, how I can use them instead of org.Hs.eg.db or org.Mm.eg.db because I am more interested in

(1) How are the gene networks that regulate differentiation affected by noise and stochasticty? (2) Do differentiating cells all follow the same path towards the differentiated state?

That I think relates to GRN analysis by your software

edroaldo commented 6 years ago

I am sorry for my deleted response. I am travelling... do you have a list of all transcription factors for your organism? If you have it, the annotations packages might not be required but I will need to update the function such that you can provide the transcription factors as a list. It might take 2-4 days to do this,if you can wait.

Thanks!

On Wed, Aug 1, 2018, 12:49 PM fereshtehizadi notifications@github.com wrote:

Sorry, there are some zip files for GO and annotation for my organism in http://dictybase.org/Downloads/, how I can use them instead of org.Hs.eg.db or org.Mm.eg.db because I am more interested in

(1) How are the gene networks that regulate differentiation affected by noise and stochasticty? (2) Do differentiating cells all follow the same path towards the differentiated state?

That I think relates to GRN analysis by your software

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edroaldo commented 6 years ago

Delayed response...

On Wed, Aug 1, 2018, 5:40 PM Edroaldo Lummertz da Rocha edroaldo@gmail.com wrote:

I am sorry for my deleted response. I am travelling... do you have a list of all transcription factors for your organism? If you have it, the annotations packages might not be required but I will need to update the function such that you can provide the transcription factors as a list. It might take 2-4 days to do this,if you can wait.

Thanks!

On Wed, Aug 1, 2018, 12:49 PM fereshtehizadi notifications@github.com wrote:

Sorry, there are some zip files for GO and annotation for my organism in http://dictybase.org/Downloads/, how I can use them instead of org.Hs.eg.db or org.Mm.eg.db because I am more interested in

(1) How are the gene networks that regulate differentiation affected by noise and stochasticty? (2) Do differentiating cells all follow the same path towards the differentiated state?

That I think relates to GRN analysis by your software

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fereshtehizadi commented 6 years ago

Please excuse me for late response to your kindly helps and offer. I will provide a list of transcription factors in my organism very soon and I will wait as much as needed to be able to try the full of this nice software on my data.

Thank you vey much

fereshtehizadi commented 6 years ago

Sorry this is a list of transcription factors (some of them are still putative) in this organism from dictyBase

TF DDB_G0267636 DDB_G0268506 DDB_G0275173 DDB_G0274697 DDB_G0275939 DDB_G0278729 DDB_G0279331 DDB_G0280547 DDB_G0282835 DDB_G0282047 DDB_G0287513 DDB_G0287057 DDB_G0286837 DDB_G0290869 DDB_G0292724 DDB_G0291197 DDB_G0269906 DDB_G0267414 DDB_G0272362 DDB_G0280627 DDB_G0280639 DDB_G0281661 DDB_G0282749 DDB_G0285139 DDB_G0289935 DDB_G0287661 DDB_G0285343 DDB_G0284201 DDB_G0286839 DDB_G0288975 DDB_G0291424 DDB_G0291075 DDB_G0285293 DDB_G0281085 DDB_G0269638 DDB_G0268920 DDB_G0270590 DDB_G0273479 DDB_G0270756 DDB_G0273127 DDB_G0273525 DDB_G0270006 DDB_G0272360 DDB_G0273545 DDB_G0279257 DDB_G0281087 DDB_G0284293 DDB_G0292782 DDB_G0288859 DDB_G0289677 DDB_G0293900 DDB_G0291348 DDB_G0294539 DDB_G0278379 DDB_G0271338 DDB_G0287337 DDB_G0277505 DDB_G0268778 DDB_G0277681 DDB_G0274993 DDB_G0274993 DDB_G0280473 DDB_G0277589 DDB_G0279439 DDB_G0281563 DDB_G0279419 DDB_G0279179 DDB_G0282499 DDB_G0282049 DDB_G0287307 DDB_G0286733 DDB_G0286391 DDB_G0292838 DDB_G0290303 DDB_G0293470 DDB_G0279377 DDB_G0269338 DDB_G0268178 DDB_G0275617 DDB_G0275445 DDB_G0280485 DDB_G0280853 DDB_G0283483 DDB_G0290169 DDB_G0292510 DDB_G0268792 DDB_G0295707 DDB_G0295787 DDB_G0267640 DDB_G0273583 DDB_G0273775 DDB_G0272967 DDB_G0278971 DDB_G0278225 DDB_G0278077 DDB_G0282811 DDB_G0282697 DDB_G0283405 DDB_G0284023 DDB_G0289651 DDB_G0290171 DDB_G0293228 DDB_G0275517 DDB_G0290929 DDB_G0270360 DDB_G0270906 DDB_G0273061 DDB_G0273645 DDB_G0275267 DDB_G0277147 DDB_G0281387 DDB_G0284129 DDB_G0284195 DDB_G0290165 DDB_G0292770 DDB_G0292242 DDB_G0291372 DDB_G0290787 DDB_G0285373 DDB_G0291342 DDB_G0268014 DDB_G0268678 DDB_G0272740 DDB_G0278321 DDB_G0278843 DDB_G0281215 DDB_G0279409 DDB_G0277591 DDB_G0281829 DDB_G0286199 DDB_G0286411 DDB_G0284183 DDB_G0286843 DDB_G0286855 DDB_G0290665 DDB_G0290491 DDB_G0290765 DDB_G0290327 DDB_G0289587 DDB_G0290173 DDB_G0279529

edroaldo commented 6 years ago

Got it! Glad to help! No problem at all! I will get this done as soon as possible.

Thanks!

On Thu, Aug 2, 2018, 11:19 AM fereshtehizadi notifications@github.com wrote:

Sorry this is a list of transcription factors in this organism

GENE DDB_G0267636 DDB_G0268506 DDB_G0279331 DDB_G0280547 DDB_G0282835 DDB_G0287057 DDB_G0286837 DDB_G0280627 DDB_G0280639 DDB_G0281661 DDB_G0285139 DDB_G0286839 DDB_G0269638 DDB_G0273479 DDB_G0270756 DDB_G0273545 DDB_G0281087 DDB_G0292782 DDB_G0279419 DDB_G0275617 DDB_G0275445 DDB_G0280853 DDB_G0283483 DDB_G0292510 DDB_G0268792 DDB_G0295707 DDB_G0267640 DDB_G0273775 DDB_G0282811 DDB_G0282697 DDB_G0289651 DDB_G0273061 DDB_G0275267 DDB_G0290787 DDB_G0285373 DDB_G0272740 DDB_G0277591 DDB_G0281829 DDB_G0286843 DDB_G0286855 DDB_G0290665

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fereshtehizadi commented 6 years ago

Sorry to make too much trouble for you and thank you so much for your attention anyway

I am working on Dictyostelium developmental stages. sampling for single cell seq has been done in 8 time points (2, 4, ...,16 hours). Text books say that we should be able to see roughly two groups of cell types at the end of development (even in each time point). By Seurat and clustering resolution 0.7 I have clustered the last time point (16 hours) to 3 clusters that by your nice software I tried out to find marker genes and trajectories in this time point. There are a few experimentally validated marker genes for cell types in this organism by which I see that in 16 hour time point I really have two groups of cells. I am going back to 14 hour , 12 hour, .., 2 hour time points to see whether genes describing each time point are the same during the time or no, in the other word how development works in this organism but I totally don't know what to do.

In your article saying Klf1 is being highly expressed in subpopulation 10, so how I could recognise genes highly expressed in each subpopulation of my cells please?

lets say I have clustered my 1500 cells in 8 time points to 9 clusters by seurat that gave me this clustering

[

](url)

CellRouter gives me this tSNE of my cells provided metadata of seurat

https://drive.google.com/file/d/1xeS_A3tf3MuT0FBrYqE8jTA4gYEuExt3/view?usp=sharing

unlike your article that you know erythroblasts, Neutrophils, etc as your population, I don't know each number (cluster) belongs to which time point. So how I can know the subpopulation for each cluster as you done in your article and genes highly expressed in each subpopulation under each cluster?

I am really very sorry for disturbing you too much

edroaldo commented 6 years ago

This is all described in the current tutorial, with the findclusters and findsignatures functions.... you can plot as a heatmap. Is that what you want? Take a look at the tutorial, cellrouter has many functions similar to the seurat ones. More details later tonight...

Thanks!

On Fri, Aug 3, 2018, 3:11 PM fereshtehizadi notifications@github.com wrote:

Thank you once again, so how could I get subpopulation underlying each cluster lets say subpopulation underlying 9 clusters as in my tSNE image and highly expressed genes of these subpopulations please?

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fereshtehizadi commented 6 years ago

Thanks a lot, for example in your article you have Neutrophil population that itself has some subpopulations, I mean for example seurat or CellRouter give me 9 clusters (name of each cluster is a number) for my 1500 cells in 8 time points; while I don’t know each number (cluster) is belong to which time point and how to identify subpopulations underlying that.

I am sorry I know most of my errors and problems come from my efficiency in R coding

edroaldo commented 6 years ago

No problem at all! Glad to help! I now understand what you want. I think you can do this using the plotProportion function available with cellrouter. You need to add your time_point info into sampTab metadata table using the addInfo() function as before. Let's let's say you call this "timepoint". Then, to check the distribution of time points per cluster or the distribution of clusters per time point, you could use:

plotProportion(cellrouter, 'seuratClusters', 'timepoint', 7, 3, filename = 'results/proportion_in_clusters.pdf')

I am sorry for my delayed response. I just moved back to my home country after my postdoc in USA.

Pleae, let me know if this is what you need.

Thanks for your patience! On Fri, Aug 3, 2018, 3:21 PM fereshtehizadi notifications@github.com wrote:

Thanks a lot, for example in your article you have Neutrophil population that itself has some subpopulations, I mean for example seurat or CellRouter give me 9 clusters (name of each cluster is a number) for my 1500 cells in 8 time points; while I don’t know each number (cluster is belong to which time point and how to identify subpopulations underlying that.

I am sorry I know most of my errors and problems come from my efficiency in R coding

On 3 Aug 2018, at 19:16, edroaldo notifications@github.com<mailto:notifications@github.com> wrote:

This is all described in the current tutorial, with the findclusters and findsignatures functions.... you can plot as a heatmap. Is that what you want? Take a look at the tutorial, cellrouter has many functions similar to the seurat ones. More details later tonight...

Thanks!

On Fri, Aug 3, 2018, 3:11 PM fereshtehizadi notifications@github.com<mailto:notifications@github.com> wrote:

Thank you once again, so how could I get subpopulation underlying each cluster lets say subpopulation underlying 9 clusters as in my tSNE image and highly expressed genes of these subpopulations please?

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edroaldo commented 6 years ago

Just use the addInfo function as you did to use your seurat clusters. Same strategy.... cannot give more details right now....

On Sun, Aug 5, 2018, 10:22 AM fereshtehizadi notifications@github.com wrote:

Sorry,

If this is the header of my time point txt file, how I can add that to my metadata?

cells time s1.1 s1.1 h16 s1.2 s1.2 h16 s1.3 s1.3 h16 s1.4 s1.4 h16 s1.5 s1.5 h16 s1.6 s1.6 h16 s1.7 s1.7 h16 s1.8 s1.8 h16 s1.9 s1.9 h16 s1.10 s1.10 h16 s1.11 s1.11 h16 s1.12 s1.12 h16 s1.13 s1.13 h16 s1.14 s1.14 h16 s1.15 s1.15 h16 s1.16 s1.16 h16 s1.17 s1.17 h16 s1.18 s1.18 h16 s1.19 s1.19 h16 s1.20 s1.20 h16 s1.21 s1.21 h16 s1.22 s1.22 h16 s1.23 s1.23 h16 s1.24 s1.24 h16 s1.25 s1.25 h16 s1.26 s1.26 h16 s1.27 s1.27 h16 s1.28 s1.28 h16 s1.29 s1.29 h16

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fereshtehizadi commented 6 years ago

Thank you, I will try :) On 5 Aug 2018, at 14:36, edroaldo notifications@github.com<mailto:notifications@github.com> wrote:

strategy

fereshtehizadi commented 6 years ago

Excuse me, apart from too much questioning from me, I am very interested in inferring GRN on my organism especially finding TFs that likely are more important in transition between cell states. So could I please ask for your kindly helps as always in inferring GRN in my organism?

Thank you very much in any case

edroaldo commented 6 years ago

I should be able to start working on this in the next 4-6 days with the list of TFs sent to me.

Thanks for your patience!

2018-08-06 12:03 GMT-04:00 fereshtehizadi notifications@github.com:

Excuse me, apart from too much questioning from me, I am very interested in inferring GRN on my organism especially finding TFs that likely are more important in transition between cell states. So could I please ask for your kindly helps as always in inferring GRN in my organism?

Thank you very much in any case

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fereshtehizadi commented 6 years ago

Actually this is me who should be thankful for kindly paying attention to my questioning

This is a list of TFs in this organism

TF DDB_G0267636 DDB_G0268506 DDB_G0275173 DDB_G0274697 DDB_G0275939 DDB_G0278729 DDB_G0279331 DDB_G0280547 DDB_G0282835 DDB_G0282047 DDB_G0287513 DDB_G0287057 DDB_G0286837 DDB_G0290869 DDB_G0292724 DDB_G0291197 DDB_G0269906 DDB_G0267414 DDB_G0272362 DDB_G0280627 DDB_G0280639 DDB_G0281661 DDB_G0282749 DDB_G0285139 DDB_G0289935 DDB_G0287661 DDB_G0285343 DDB_G0284201 DDB_G0286839 DDB_G0288975 DDB_G0291424 DDB_G0291075 DDB_G0285293 DDB_G0281085 DDB_G0269638 DDB_G0268920 DDB_G0270590 DDB_G0273479 DDB_G0270756 DDB_G0273127 DDB_G0273525 DDB_G0270006 DDB_G0272360 DDB_G0273545 DDB_G0279257 DDB_G0281087 DDB_G0284293 DDB_G0292782 DDB_G0288859 DDB_G0289677 DDB_G0293900 DDB_G0291348 DDB_G0294539 DDB_G0278379 DDB_G0271338 DDB_G0287337 DDB_G0277505 DDB_G0268778 DDB_G0277681 DDB_G0274993 DDB_G0274993 DDB_G0280473 DDB_G0277589 DDB_G0279439 DDB_G0281563 DDB_G0279419 DDB_G0279179 DDB_G0282499 DDB_G0282049 DDB_G0287307 DDB_G0286733 DDB_G0286391 DDB_G0292838 DDB_G0290303 DDB_G0293470 DDB_G0279377 DDB_G0269338 DDB_G0268178 DDB_G0275617 DDB_G0275445 DDB_G0280485 DDB_G0280853 DDB_G0283483 DDB_G0290169 DDB_G0292510 DDB_G0268792 DDB_G0295707 DDB_G0295787 DDB_G0267640 DDB_G0273583 DDB_G0273775 DDB_G0272967 DDB_G0278971 DDB_G0278225 DDB_G0278077 DDB_G0282811 DDB_G0282697 DDB_G0283405 DDB_G0284023 DDB_G0289651 DDB_G0290171 DDB_G0293228 DDB_G0275517 DDB_G0290929 DDB_G0270360 DDB_G0270906 DDB_G0273061 DDB_G0273645 DDB_G0275267 DDB_G0277147 DDB_G0281387 DDB_G0284129 DDB_G0284195 DDB_G0290165 DDB_G0292770 DDB_G0292242 DDB_G0291372 DDB_G0290787 DDB_G0285373 DDB_G0291342 DDB_G0268014 DDB_G0268678 DDB_G0272740 DDB_G0278321 DDB_G0278843 DDB_G0281215 DDB_G0279409 DDB_G0277591 DDB_G0281829 DDB_G0286199 DDB_G0286411 DDB_G0284183 DDB_G0286843 DDB_G0286855 DDB_G0290665 DDB_G0290491 DDB_G0290765 DDB_G0290327 DDB_G0289587 DDB_G0290173 DDB_G0279529

fereshtehizadi commented 6 years ago

Excuse me to be too bold to disturb you so much

has been possible for you to help me inferring GRN in this specific organism I am working on?

Thank you so much in advance

edroaldo commented 6 years ago

I am sorry for the delay but I still did not have a chance to get started on this. Please give me 2 more days and this should be done...

Thanks!

On Mon, Aug 13, 2018, 2:31 PM fereshtehizadi notifications@github.com wrote:

Excuse me to be too bold to disturb you so much

has been possible for you to help me inferring GRN in this specific organism I am working on?

Thank you so much in advance

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fereshtehizadi commented 6 years ago

Please don't mention like this because this is me who should be sorry :(

Thank you very much

edroaldo commented 6 years ago

Hi,

Finally... So, I will not be able to release a new cellrouter version with these changes because I am still working on additional features but you can create a gene regulatory network for your organism using the the buildGRN2 function below. Basically, copy and paste the function below in the CellRouter_Class.R file and do your analysis as before. You can use tfs to provide your list of transcription factors.

' Predict a gene regulatory network. It allows a customized list of

transcription factors or genes (tfs)

' @param object CellRouter object

' @param species species

' @param tfs list of transcription factors to use for GRN reconstruction

' @param genes.use genes to include in the gene regulatory network

' @param zscore zscore threshold to identify putative regulatory

interactions

' @param filename filename of GRN data

' @export

setGeneric("buildGRN2", function(object, species, tfs=NULL, genes.use=NULL, zscore=5, filename='GRN.R') standardGeneric("buildGRN2")) setMethod("buildGRN2", signature = "CellRouter", definition = function(object, species, tfs, genes.use, zscore=5, filename='GRN.R'){ if(is.null(genes.use)){ genes.use <- rownames(object@ndata) } if(is.null(tfs)){ tfs <- find_tfs(species = species) } grn <- globalGRN(object@ndata[genes.use,], tfs, zscore) colnames(grn)[1:2]<-c("TG", "TF"); ggrn<- ig_tabToIgraph(grn, simplify = TRUE) x <- list(GRN=ggrn, GRN_table=grn, tfs=tfs) save(x, file=filename)

        return(x)
      }

)

Then, you can use this function to reconstruct a GRN for your organism using: grn.data <- buildGRN2(cellrouter, tfs=yourTFs, genes.use = rownames(cellrouter@ndata), zscore = 5, filename = 'GRN_custom_TFs.R')

Where yourTFs is your list of transcription factors that you sent me ealier. It should be a vector of gene names. Please, give it a try and let me know if that works for you. The other analysis should be fine...

Thanks a lot!

Em seg, 13 de ago de 2018 às 14:09, fereshtehizadi notifications@github.com escreveu:

Please don't mention like this because this is me who should be sorry :(

Thank you very much

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fereshtehizadi commented 6 years ago

Thanks a lot for your kindly helps

I just copied and pasted your function in last line of CellRouter_Class.R file then 

> source('CellRouter_Class.R')
Error in source("CellRouter_Class.R") : 
  CellRouter_Class.R:2994:15: unexpected symbol
2993: #' Predict a gene regulatory network. It allows a customized list of
2994: transcription factors
                    ^
edroaldo commented 6 years ago

Oh... need to remove the documentation comments...

Try this: setGeneric("buildGRN2", function(object, species, tfs=NULL, genes.use=NULL, zscore=5, filename='GRN.R') standardGeneric("buildGRN2")) setMethod("buildGRN2", signature = "CellRouter", definition = function(object, species, tfs, genes.use, zscore=5, filename='GRN.R'){ if(is.null(genes.use)){ genes.use <- rownames(object@ndata) } if(is.null(tfs)){ tfs <- find_tfs(species = species) } grn <- globalGRN(object@ndata[genes.use,], tfs, zscore) colnames(grn)[1:2]<-c("TG", "TF"); ggrn<- ig_tabToIgraph(grn, simplify = TRUE) x <- list(GRN=ggrn, GRN_table=grn, tfs=tfs) save(x, file=filename)

        return(x)
      }

) Thanks!

Em qua, 15 de ago de 2018 às 09:22, fereshtehizadi notifications@github.com escreveu:

Thanks a lot for your kindly helps

I just copied and pasted your function in last line of CellRouter_Class.R file then

source('CellRouter_Class.R') Error in source("CellRouter_Class.R") : CellRouter_Class.R:2994:15: unexpected symbol 2993: #' Predict a gene regulatory network. It allows a customized list of 2994: transcription factors ^

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fereshtehizadi commented 6 years ago

Thanks a lot, function worked I am going to try GRN inferring on my data 

> source('CellRouter_Class.R')
>
edroaldo commented 6 years ago

OK...

Good luck!

Em qua, 15 de ago de 2018 às 09:28, fereshtehizadi notifications@github.com escreveu:

Thanks a lot, function worked I am going to try GRN inferring on my data

source('CellRouter_Class.R')

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fereshtehizadi commented 6 years ago

Thanks a lot, I read my TFs

> TF=as.vector(TF)
> is.vector(TF)
[1] TRUE
> grn.data <- buildGRN2(cellrouter, tfs=TF, genes.use =
+                           rownames(cellrouter@ndata), zscore = 5, filename = 'GRN_custom_TFs.R')
2723 2723 
2723 2723 

> grn.data <- get(load('GRN_custom_TFs.R'))
> transitions <- c('0.1','0.2') #transitions to be analyzed
> grn.scores <- grnscores(cellrouter, ggrn = grn.data$GRN, tfs = grn.data$tfs, transitions = transitions, direction='both', flip=TRUE, q.up=0.75, q.down=0.25,
+                         dir.targets='up', columns=2, width=5, height=7, filename='results/GRN_scores')
 Show Traceback

 Rerun with Debug
 Error: $ operator is invalid for atomic vectors In addition: Warning messages:
1: In min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
2: In max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
> grn.data <- get(load('GRN_custom_TFs.R'))
> transitions <- c('0.1','0.2') #transitions to be analyzed
> grn.scores <- grnscores(cellrouter, ggrn = grn.data$GRN, tfs = grn.data$tfs, transitions = transitions, direction='both', flip=TRUE, q.up=0.75, q.down=0.25,
+                         dir.targets='up', columns=2, width=5, height=7, filename='results/GRN_scores')
 Show Traceback

 Rerun with Debug
 Error: $ operator is invalid for atomic vectors In addition: Warning messages:
1: In min(x, na.rm = na.rm) :
  no non-missing arguments to min; returning Inf
2: In max(x, na.rm = na.rm) :
  no non-missing arguments to max; returning -Inf
>
edroaldo commented 6 years ago

hum... can you please show me this output: grn.data$GRN grn.data$tfs

Thanks!

Em qua, 15 de ago de 2018 às 09:46, fereshtehizadi notifications@github.com escreveu:

Thanks a lot, I read my TFs

TF=as.vector(TF) is.vector(TF) [1] TRUE grn.data <- buildGRN2(cellrouter, tfs=TF, genes.use =

  • rownames(cellrouter@ndata), zscore = 5, filename = 'GRN_custom_TFs.R') 2723 2723 2723 2723

grn.data <- get(load('GRN_custom_TFs.R')) transitions <- c('0.1','0.2') #transitions to be analyzed grn.scores <- grnscores(cellrouter, ggrn = grn.data$GRN, tfs = grn.data$tfs, transitions = transitions, direction='both', flip=TRUE, q.up=0.75, q.down=0.25,

  • dir.targets='up', columns=2, width=5, height=7, filename='results/GRN_scores') Show Traceback

Rerun with Debug Error: $ operator is invalid for atomic vectors In addition: Warning messages: 1: In min(x, na.rm = na.rm) : no non-missing arguments to min; returning Inf 2: In max(x, na.rm = na.rm) : no non-missing arguments to max; returning -Inf

grn.data <- get(load('GRN_custom_TFs.R')) transitions <- c('0.1','0.2') #transitions to be analyzed grn.scores <- grnscores(cellrouter, ggrn = grn.data$GRN, tfs = grn.data$tfs, transitions = transitions, direction='both', flip=TRUE, q.up=0.75, q.down=0.25,

  • dir.targets='up', columns=2, width=5, height=7, filename='results/GRN_scores') Show Traceback

Rerun with Debug Error: $ operator is invalid for atomic vectors In addition: Warning messages: 1: In min(x, na.rm = na.rm) : no non-missing arguments to min; returning Inf 2: In max(x, na.rm = na.rm) : no non-missing arguments to max; returning -Inf

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fereshtehizadi commented 6 years ago

Thanks a lot,

> grn.data$GRN
IGRAPH a0b4b97 UNWB 230 232 -- 
+ attr: name (v/c), label (v/c), type (v/c), nEnts (v/n), weight (e/n)
+ edges from a0b4b97 (vertex names):
 [1] DDB_G0291348--DDB_G0267378 DDB_G0291348--DDB_G0268204 DDB_G0291348--DDB_G0273077 DDB_G0291348--DDB_G0273767 DDB_G0291348--DDB_G0275687 DDB_G0291348--DDB_G0275753
 [7] DDB_G0291348--DDB_G0278171 DDB_G0291348--DDB_G0280433 DDB_G0291348--DDB_G0289861 DDB_G0291348--DDB_G0295653 DDB_G0279529--DDB_G0267436 DDB_G0279529--DDB_G0288951
[13] DDB_G0277681--DDB_G0267454 DDB_G0277681--DDB_G0269234 DDB_G0277681--DDB_G0272250 DDB_G0277681--DDB_G0275881 DDB_G0277681--DDB_G0279207 DDB_G0277681--DDB_G0282601
[19] DDB_G0277681--DDB_G0285881 DDB_G0277681--DDB_G0286117 DDB_G0277681--DDB_G0289877 DDB_G0277589--DDB_G0267458 DDB_G0277589--DDB_G0278959 DDB_G0277589--DDB_G0279667
[25] DDB_G0277589--DDB_G0279951 DDB_G0277589--DDB_G0284177 DDB_G0277589--DDB_G0288295 DDB_G0277589--DDB_G0292460 DDB_G0293900--DDB_G0273645 DDB_G0293900--DDB_G0267730
[31] DDB_G0293900--DDB_G0283325 DDB_G0268014--DDB_G0267792 DDB_G0268014--DDB_G0268638 DDB_G0268014--DDB_G0268882 DDB_G0268014--DDB_G0276475 DDB_G0268014--DDB_G0276789
[37] DDB_G0268014--DDB_G0277253 DDB_G0268014--DDB_G0277789 DDB_G0268014--DDB_G0284345 DDB_G0268014--DDB_G0290503 DDB_G0268014--DDB_G0293532 DDB_G0287661--DDB_G0268638
[43] DDB_G0287661--DDB_G0268882 DDB_G0287661--DDB_G0269140 DDB_G0287661--DDB_G0277789 DDB_G0287661--DDB_G0283767 DDB_G0287661--DDB_G0288123 DDB_G0287661--DDB_G0291568
+ ... omitted several edges
> 
> grn.data$tfs
  [1] "DDB_G0268506" "DDB_G0275173" "DDB_G0274697" "DDB_G0275939" "DDB_G0278729" "DDB_G0279331" "DDB_G0280547" "DDB_G0282835" "DDB_G0282047" "DDB_G0287513" "DDB_G0287057"
 [12] "DDB_G0286837" "DDB_G0290869" "DDB_G0292724" "DDB_G0291197" "DDB_G0269906" "DDB_G0267414" "DDB_G0272362" "DDB_G0280627" "DDB_G0280639" "DDB_G0281661" "DDB_G0282749"
 [23] "DDB_G0285139" "DDB_G0289935" "DDB_G0287661" "DDB_G0285343" "DDB_G0284201" "DDB_G0286839" "DDB_G0288975" "DDB_G0291424" "DDB_G0291075" "DDB_G0285293" "DDB_G0281085"
 [34] "DDB_G0269638" "DDB_G0268920" "DDB_G0270590" "DDB_G0273479" "DDB_G0270756" "DDB_G0273127" "DDB_G0273525" "DDB_G0270006" "DDB_G0272360" "DDB_G0273545" "DDB_G0279257"
 [45] "DDB_G0281087" "DDB_G0284293" "DDB_G0292782" "DDB_G0288859" "DDB_G0289677" "DDB_G0293900" "DDB_G0291348" "DDB_G0294539" "DDB_G0278379" "DDB_G0271338" "DDB_G0287337"
 [56] "DDB_G0277505" "DDB_G0268778" "DDB_G0277681" "DDB_G0274993" "DDB_G0274993" "DDB_G0280473" "DDB_G0277589" "DDB_G0279439" "DDB_G0281563" "DDB_G0279419" "DDB_G0279179"
 [67] "DDB_G0282499" "DDB_G0282049" "DDB_G0287307" "DDB_G0286733" "DDB_G0286391" "DDB_G0292838" "DDB_G0290303" "DDB_G0293470" "DDB_G0279377" "DDB_G0269338" "DDB_G0268178"
 [78] "DDB_G0275617" "DDB_G0275445" "DDB_G0280485" "DDB_G0280853" "DDB_G0283483" "DDB_G0290169" "DDB_G0292510" "DDB_G0268792" "DDB_G0295707" "DDB_G0295787" "DDB_G0267640"
 [89] "DDB_G0273583" "DDB_G0273775" "DDB_G0272967" "DDB_G0278971" "DDB_G0278225" "DDB_G0278077" "DDB_G0282811" "DDB_G0282697" "DDB_G0283405" "DDB_G0284023" "DDB_G0289651"
[100] "DDB_G0290171" "DDB_G0293228" "DDB_G0275517" "DDB_G0290929" "DDB_G0270360" "DDB_G0270906" "DDB_G0273061" "DDB_G0273645" "DDB_G0275267" "DDB_G0277147" "DDB_G0281387"
[111] "DDB_G0284129" "DDB_G0284195" "DDB_G0290165" "DDB_G0292770" "DDB_G0292242" "DDB_G0291372" "DDB_G0290787" "DDB_G0285373" "DDB_G0291342" "DDB_G0268014" "DDB_G0268678"
[122] "DDB_G0272740" "DDB_G0278321" "DDB_G0278843" "DDB_G0281215" "DDB_G0279409" "DDB_G0277591" "DDB_G0281829" "DDB_G0286199" "DDB_G0286411" "DDB_G0284183" "DDB_G0286843"
[133] "DDB_G0286855" "DDB_G0290665" "DDB_G0290491" "DDB_G0290765" "DDB_G0290327" "DDB_G0289587" "DDB_G0290173" "DDB_G0279529"
> 
>
edroaldo commented 6 years ago

It looks fine... can you please show me the content of "names" names <- unique(names(cellrouter@pathsinfo$distr))

Thanks!

Em qua, 15 de ago de 2018 às 09:54, fereshtehizadi notifications@github.com escreveu:

Thanks a lot,

grn.data$GRN IGRAPH a0b4b97 UNWB 230 232 --

  • attr: name (v/c), label (v/c), type (v/c), nEnts (v/n), weight (e/n)
  • edges from a0b4b97 (vertex names): [1] DDB_G0291348--DDB_G0267378 DDB_G0291348--DDB_G0268204 DDB_G0291348--DDB_G0273077 DDB_G0291348--DDB_G0273767 DDB_G0291348--DDB_G0275687 DDB_G0291348--DDB_G0275753 [7] DDB_G0291348--DDB_G0278171 DDB_G0291348--DDB_G0280433 DDB_G0291348--DDB_G0289861 DDB_G0291348--DDB_G0295653 DDB_G0279529--DDB_G0267436 DDB_G0279529--DDB_G0288951 [13] DDB_G0277681--DDB_G0267454 DDB_G0277681--DDB_G0269234 DDB_G0277681--DDB_G0272250 DDB_G0277681--DDB_G0275881 DDB_G0277681--DDB_G0279207 DDB_G0277681--DDB_G0282601 [19] DDB_G0277681--DDB_G0285881 DDB_G0277681--DDB_G0286117 DDB_G0277681--DDB_G0289877 DDB_G0277589--DDB_G0267458 DDB_G0277589--DDB_G0278959 DDB_G0277589--DDB_G0279667 [25] DDB_G0277589--DDB_G0279951 DDB_G0277589--DDB_G0284177 DDB_G0277589--DDB_G0288295 DDB_G0277589--DDB_G0292460 DDB_G0293900--DDB_G0273645 DDB_G0293900--DDB_G0267730 [31] DDB_G0293900--DDB_G0283325 DDB_G0268014--DDB_G0267792 DDB_G0268014--DDB_G0268638 DDB_G0268014--DDB_G0268882 DDB_G0268014--DDB_G0276475 DDB_G0268014--DDB_G0276789 [37] DDB_G0268014--DDB_G0277253 DDB_G0268014--DDB_G0277789 DDB_G0268014--DDB_G0284345 DDB_G0268014--DDB_G0290503 DDB_G0268014--DDB_G0293532 DDB_G0287661--DDB_G0268638 [43] DDB_G0287661--DDB_G0268882 DDB_G0287661--DDB_G0269140 DDB_G0287661--DDB_G0277789 DDB_G0287661--DDB_G0283767 DDB_G0287661--DDB_G0288123 DDB_G0287661--DDB_G0291568
  • ... omitted several edges

grn.data$tfs [1] "DDB_G0268506" "DDB_G0275173" "DDB_G0274697" "DDB_G0275939" "DDB_G0278729" "DDB_G0279331" "DDB_G0280547" "DDB_G0282835" "DDB_G0282047" "DDB_G0287513" "DDB_G0287057" [12] "DDB_G0286837" "DDB_G0290869" "DDB_G0292724" "DDB_G0291197" "DDB_G0269906" "DDB_G0267414" "DDB_G0272362" "DDB_G0280627" "DDB_G0280639" "DDB_G0281661" "DDB_G0282749" [23] "DDB_G0285139" "DDB_G0289935" "DDB_G0287661" "DDB_G0285343" "DDB_G0284201" "DDB_G0286839" "DDB_G0288975" "DDB_G0291424" "DDB_G0291075" "DDB_G0285293" "DDB_G0281085" [34] "DDB_G0269638" "DDB_G0268920" "DDB_G0270590" "DDB_G0273479" "DDB_G0270756" "DDB_G0273127" "DDB_G0273525" "DDB_G0270006" "DDB_G0272360" "DDB_G0273545" "DDB_G0279257" [45] "DDB_G0281087" "DDB_G0284293" "DDB_G0292782" "DDB_G0288859" "DDB_G0289677" "DDB_G0293900" "DDB_G0291348" "DDB_G0294539" "DDB_G0278379" "DDB_G0271338" "DDB_G0287337" [56] "DDB_G0277505" "DDB_G0268778" "DDB_G0277681" "DDB_G0274993" "DDB_G0274993" "DDB_G0280473" "DDB_G0277589" "DDB_G0279439" "DDB_G0281563" "DDB_G0279419" "DDB_G0279179" [67] "DDB_G0282499" "DDB_G0282049" "DDB_G0287307" "DDB_G0286733" "DDB_G0286391" "DDB_G0292838" "DDB_G0290303" "DDB_G0293470" "DDB_G0279377" "DDB_G0269338" "DDB_G0268178" [78] "DDB_G0275617" "DDB_G0275445" "DDB_G0280485" "DDB_G0280853" "DDB_G0283483" "DDB_G0290169" "DDB_G0292510" "DDB_G0268792" "DDB_G0295707" "DDB_G0295787" "DDB_G0267640" [89] "DDB_G0273583" "DDB_G0273775" "DDB_G0272967" "DDB_G0278971" "DDB_G0278225" "DDB_G0278077" "DDB_G0282811" "DDB_G0282697" "DDB_G0283405" "DDB_G0284023" "DDB_G0289651" [100] "DDB_G0290171" "DDB_G0293228" "DDB_G0275517" "DDB_G0290929" "DDB_G0270360" "DDB_G0270906" "DDB_G0273061" "DDB_G0273645" "DDB_G0275267" "DDB_G0277147" "DDB_G0281387" [111] "DDB_G0284129" "DDB_G0284195" "DDB_G0290165" "DDB_G0292770" "DDB_G0292242" "DDB_G0291372" "DDB_G0290787" "DDB_G0285373" "DDB_G0291342" "DDB_G0268014" "DDB_G0268678" [122] "DDB_G0272740" "DDB_G0278321" "DDB_G0278843" "DDB_G0281215" "DDB_G0279409" "DDB_G0277591" "DDB_G0281829" "DDB_G0286199" "DDB_G0286411" "DDB_G0284183" "DDB_G0286843" [133] "DDB_G0286855" "DDB_G0290665" "DDB_G0290491" "DDB_G0290765" "DDB_G0290327" "DDB_G0289587" "DDB_G0290173" "DDB_G0279529"

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fereshtehizadi commented 6 years ago

Thanks a lot


names <- unique(names(cellrouter@pathsinfo$distr))

chr [1:2] "2:1" "2:0"
fereshtehizadi commented 6 years ago

Sorry, I think the problem was I was not saving filename = 'GRN_custom_TFs.R' in my results file. Code worked I obtained regulators, only at the end of tutorial I faced this

> regulators <- c('DDB_G0267412')
> nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf')
Error in l[which(l$type == "Regulator"), ] : 
  incorrect number of dimensions
> regulators <- c('DDB_G0267412','DDB_G0277853')
> nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf')
Error in l[which(l$type == "Regulator"), ] : 
  incorrect number of dimensions

> regulators <- c('DDB_G0279419','DDB_G0286411','DDB_G0281829')
> nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf')
 Show Traceback

 Rerun with Debug
 Error in if (params$fiteach) { : argument is not interpretable as logical In addition: Warning message:
In if (params$fiteach) { :
  the condition has length > 1 and only the first element will be used
>
edroaldo commented 6 years ago

That's strange... and potentially the source of your error. This should be something like '0.1', '0.2', and so on:

grn.data <- get(load('GRN_custom_TFs.R')) transitions <- c('0.1','0.2') #transitions to be analyzed

Moreover, it is strange that the name convention that cellrouter uses is not represented in this output. When you select cluster 2 as starting point and cluster 1 as an endpoint of the trajectory, this should never be "2:1", it should be "2.1". So, I am not sure what you are doing...

Can you send me your tsne map again and also the content of sources and targets (just before your call to the findPaths function)?

sources <- c('3')targets <- setdiff(unique(cellrouter@sampTab$population), sources)methods <- c("euclidean", "maximum", "manhattan","canberra","binary", 'graph')

graph for distances in KNN

cellrouter <- findPaths(cellrouter, column='population', libdir, paste(getwd(), 'results/paths', sep='/'), method="graph")

Basically, your "transitions" should be the same as "names". If everything is correct, you should have, but again, trajectory names should not have a ":" as a seperator... Really not sure what you did...

transitions <- c('2:1','2:0')

Thanks!

Em qua, 15 de ago de 2018 às 09:58, fereshtehizadi notifications@github.com escreveu:

Thanks a lot

names <- unique(names(cellrouter@pathsinfo$distr))

chr [1:2] "2:1" "2:0"

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edroaldo commented 6 years ago

Did the previous plot work? The one using the grnscores function? Can you send it to me? Is your list of regulators in "regulators" among the ones that show up in the grnscores function? Do you have the package below installed?

library('geomnet')

Em qua, 15 de ago de 2018 às 10:12, fereshtehizadi notifications@github.com escreveu:

Sorry, I think the problem was I was not saving filename = 'GRN_custom_TFs.R' in my results file. Code worked I obtained regulators, only at the end of tutorial I faced this

regulators <- c('DDB_G0267412') nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf') Error in l[which(l$type == "Regulator"), ] : incorrect number of dimensions regulators <- c('DDB_G0267412','DDB_G0277853') nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf') Error in l[which(l$type == "Regulator"), ] : incorrect number of dimensions

regulators <- c('DDB_G0279419','DDB_G0286411','DDB_G0281829') nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf') Show Traceback

Rerun with Debug Error in if (params$fiteach) { : argument is not interpretable as logical In addition: Warning message: In if (params$fiteach) { : the condition has length > 1 and only the first element will be used

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fereshtehizadi commented 6 years ago

Thanks a lot, yes I run library('geomnet’) beforehand

These are the link to produced images

https://drive.google.com/file/d/1V6VeZES88jF8JfFqY3OLXIg5n7VqEFjC/view?usp=sharing

https://drive.google.com/file/d/1-Izh8XXKlLLLXO1uRxlcwTQnNZZ--PBE/view?usp=sharing

On 15 Aug 2018, at 15:21, edroaldo notifications@github.com<mailto:notifications@github.com> wrote:

Did the previous plot work? The one using the grnscores function? Can you send it to me? Is your list of regulators in "regulators" among the ones that show up in the grnscores function? Do you have the package below installed?

library('geomnet')

Em qua, 15 de ago de 2018 às 10:12, fereshtehizadi notifications@github.com<mailto:notifications@github.com> escreveu:

Sorry, I think the problem was I was not saving filename = 'GRN_custom_TFs.R' in my results file. Code worked I obtained regulators, only at the end of tutorial I faced this

regulators <- c('DDB_G0267412') nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf') Error in l[which(l$type == "Regulator"), ] : incorrect number of dimensions regulators <- c('DDB_G0267412','DDB_G0277853') nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf') Error in l[which(l$type == "Regulator"), ] : incorrect number of dimensions

regulators <- c('DDB_G0279419','DDB_G0286411','DDB_G0281829') nets1 <- regulatornetwork(grn.scores, grn.data$GRN,regulators, 5, 2, 5, 9, 'results/regulator_networks_1.pdf') Show Traceback

Rerun with Debug Error in if (params$fiteach) { : argument is not interpretable as logical In addition: Warning message: In if (params$fiteach) { : the condition has length > 1 and only the first element will be used

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