I am getting all error when coming back to cellrouter after a year

[beginner984]

Hi

I am using Paul data as a toy but I am getting error :(

> plotReducedDimension(cellrouter, reduction.type = 'tsne', annotation="population", annotation.color = 'colors',showlabels = TRUE, width = 4.5, height = 3.5, filename='results/tSNE_graphClustering_clusters.pdf')
 Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : 
  replacement has 0 rows, data has 2699 
> plotReducedDimension(cellrouter, reduction.type = 'tsne', annotation="celltype", annotation.color = 'celltype',showlabels = TRUE, width = 4.5, height = 3.5, filename='results/tSNE_graphClustering_clusters.pdf')
 Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'CMP' 
> plotReducedDimension(cellrouter, reduction.type = 'pca', annotation="celltype", annotation.color = 'celltype',showlabels = TRUE, width = 4.5, height = 3.5, filename='results/tSNE_graphClustering_clusters.pdf')
 Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'CMP' 

Can you help please?

[edroaldo]

Hi,

It seems that rownames(cellrouter@sampTab) and colnames(cellrouter@ndata) does not match. Are you following the tutorial step-by-step? Can you please send me the commands you are using? If you used the files I provided in github this should not be happening.

Thanks!

On Mon, Oct 21, 2019 at 6:33 AM beginner984 notifications@github.com wrote:

Hi

I am using Paul data as a toy but I am getting error :(

plotReducedDimension(cellrouter, reduction.type = 'tsne', annotation="population", annotation.color = 'colors',showlabels = TRUE, width = 4.5, height = 3.5, filename='results/tSNE_graphClustering_clusters.pdf') Error in $<-.data.frame(*tmp*, "group", value = integer(0)) : replacement has 0 rows, data has 2699 plotReducedDimension(cellrouter, reduction.type = 'tsne', annotation="celltype", annotation.color = 'celltype',showlabels = TRUE, width = 4.5, height = 3.5, filename='results/tSNE_graphClustering_clusters.pdf') Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'CMP' plotReducedDimension(cellrouter, reduction.type = 'pca', annotation="celltype", annotation.color = 'celltype',showlabels = TRUE, width = 4.5, height = 3.5, filename='results/tSNE_graphClustering_clusters.pdf') Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'CMP'

Can you help please?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/edroaldo/cellrouter/issues/28?email_source=notifications&email_token=ACNJIR5D2A5XZCQJRJVF7YDQPWAN3A5CNFSM4JC3LU32YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HTEC23Q, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACNJIR4JRWU45BJDYEIHDQTQPWAN3ANCNFSM4JC3LU3Q .

-- Edroaldo

[beginner984]

Thank you for answering me

I was trying in windows suddenly I saw you are mentioning that your software not working in windows so I changed to Linux but at the first step I have been stopped

This is the version of my R

> version
               _                           
platform       x86_64-unknown-linux-gnu    
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          2.1                         
year           2015                        
month          06                          
day            18                          
svn rev        68531                       
language       R                           
version.string R version 3.2.1 (2015-06-18)
nickname       World-Famous Astronaut 

For reading Paul R object in R I tried a lot but all error

    > cellrouter <- CellRouter(path='Paul_Cell_data.R', min.cells=3, min.genes=0)
    Error in initialize(value, ...) : 
      invalid names for slots of class “CellRouter”: path, min.cells, min.genes
    > cellrouter <- CellRouter(read.table("Paul_Cell_data.R"), min.cells=3, min.genes=0)
    Error in initialize(value, ...) : 
      cannot use object of class “data.frame” in new():  class “CellRouter” does not extend that class
    In addition: Warning messages:
    1: In read.table("Paul_Cell_data.R") :
      line 3 appears to contain embedded nulls
    2: In read.table("Paul_Cell_data.R") :
      line 4 appears to contain embedded nulls
    3: In read.table("Paul_Cell_data.R") :
      line 5 appears to contain embedded nulls
    4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
      embedded nul(s) found in input
    > cellrouter <- CellRouter(as.matrix(read.table("Paul_Cell_data.R")), min.cells=3, min.genes=0)
    Error in initialize(value, ...) : 
      cannot use object of class “matrix” in new():  class “CellRouter” does not extend that class
    In addition: Warning messages:
    1: In read.table("Paul_Cell_data.R") :
      line 3 appears to contain embedded nulls
    2: In read.table("Paul_Cell_data.R") :
      line 4 appears to contain embedded nulls
    3: In read.table("Paul_Cell_data.R") :
      line 5 appears to contain embedded nulls
    4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
      embedded nul(s) found in input

Can somebody please help me?