What does this error mean

[beginner984]

Hello

I am getting this error

> str(SV)
'data.frame':   3904 obs. of  10 variables:
 $ Sample        : chr  "CHC018T" "CHC018T" "CHC018T" "CHC018T" ...
 $ Type          : Factor w/ 4 levels "BND","DEL","DUP",..: 1 1 1 1 2 1 2 4 4 1 ...
 $ CHROM_1       : Factor w/ 24 levels "chr1","chr10",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ POS_1         : int  753734 753747 20344587 35059560 71153953 73145906 154268027 239675118 240764937 243095807 ...
 $ CHROM_2       : Factor w/ 24 levels "chr1","chr10",..: 21 21 20 21 1 19 1 1 1 24 ...
 $ POS_2         : int  327403 327385 8707723 113025415 71154456 90830514 154270067 239702870 240919366 13952430 ...
 $ Tumor_Varcount: int  22 17 24 51 34 181 24 137 91 29 ...
 $ Tumor_Depth   : int  52 37 163 219 228 428 420 384 288 170 ...
 $ Normal_Depth  : int  101 104 63 172 261 304 161 274 322 89 ...
 $ Driver        : Factor w/ 15 levels "ACVR2A DEL","ALB DEL",..: NA NA NA NA NA NA NA NA NA NA ...
> SV.vcf <- preprocessInput_sv(input_data =  SV,resdir = getwd())
[1] "Annotating mutation data:"
  |======================================================================| 100%
[1] "CHC018T"
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(cyto[which(cyto$Chromosome == sub("chr", "", chr)), "Start"]) :
  no non-missing arguments to min; returning Inf
2: In max(cyto[which(cyto$Chromosome == sub("chr", "", chr)), "End"]) :
  no non-missing arguments to max; returning -Inf
> 

[jayendrashinde91]

Hi beginner984, Kindly make sure you convert the data.frame columns from factors/int to default formats that are provided in our example dataset:

str(SV_data) 'data.frame': 3904 obs. of 10 variables: $ Sample : chr "CHC018T" "CHC018T" "CHC018T" "CHC018T" ... $ Type : chr "BND" "BND" "BND" "BND" ... $ CHROM_1 : chr "chr1" "chr1" "chr1" "chr1" ... $ POS_1 : num 753734 753747 20344587 35059560 71153953 ... $ CHROM_2 : chr "chr8" "chr8" "chr7" "chr8" ... $ POS_2 : num 3.27e+05 3.27e+05 8.71e+06 1.13e+08 7.12e+07 ... $ Tumor_Varcount: num 22 17 24 51 34 181 24 137 91 29 ... $ Tumor_Depth : num 52 37 163 219 228 428 420 384 288 170 ... $ Normal_Depth : num 101 104 63 172 261 304 161 274 322 89 ... $ Driver : chr NA NA NA NA ...

[beginner984]

Thank you @FunGeST @jayendrashinde91 that worked

As this part needs bedtools and I could not install bedtools on my laptop, I therefore used our cluster computing nodes to get the first part of SV analysis I then saved work place as image and carried on my personal laptop but here after I am getting this error likely on SV_col

> load("~/Downloads/my_work_space.RData")
> SVsignatures_exp <- deconvolution_fit_SV(vcf = SV.vcf,
+                                          input_data = SV_input$mut_props,
+                                          input_signatures = denovo_signatures,
+                                          sig_cols = SV_cols,
+                                          resdir =getwd())
[1] "CHC018T"

RCircos.Core.Components initialized.
Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

Error in pie(t(prop.sigs.), labels = rownames(prop.sigs.), explode = 0.1,  : 
  object 'SV_cols' not found
In addition: Warning message:
In sig.fit$res.x/sig.tot :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

> 

### And when I carry on the cluster machine I get this

> SVsignatures_exp <- deconvolution_fit_SV(vcf = SV.vcf,input_data = SV_input$mut_props,input_signatures = SV_denovo_sigs,sig_cols = SV_cols,resdir = '/home/fi1d18/new')
[1] "CHC018T"

RCircos.Core.Components initialized.
Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.

Error in .External2(C_X11, paste0("png::", filename), g$width, g$height,  : 
  unable to start device PNG
In addition: Warning message:
In png(file.path(resdir, paste0("Circos_", Sample_to_plot, ".png")),  :
  unable to open connection to X11 display ''
> 

[jayendrashinde91]

@beginner984 - These are not issues related to Palimpsest.

Please check how you are transferring the workspace and objects related to your analysis back and forth between different systems.

1. Object 'SV_cols' not found = the object SV_cols is not loaded properly or is missing.

2. There's no X11 server on your cluster which is the reason for the error in rendering PNG files output. You can use the arguments plot = FALSE to avoid PNG rendering on your cluster.

SVsignatures_exp <- deconvolution_fit_SV(vcf = SV.vcf,input_data = SV_input$mut_props,input_signatures = SV_denovo_sigs,sig_cols = SV_cols,resdir = '/home/fi1d18/new', plot=FALSE)

[beginner984]

Sorry

People say that

options(bitmapType='cairo') would fix the problem but I am not sure where I should add this line ti the R script

I have load Cairo R package itself which did not help