Palimpsest
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What does this error mean
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
>
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 ...
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$height, :
unable to start device PNG
In addition: Warning message:
In png(file.path(resdir, paste0("Circos_", Sample_to_plot, ".png")), :
unable to open connection to X11 display ''
>
@beginner984 - These are not issues related to Palimpsest.
Please check how you are transferring the workspace and objects related to your analysis back and forth between different systems.
-
Object 'SV_cols' not found = the object SV_cols is not loaded properly or is missing.
-
There's no X11 server on your cluster which is the reason for the error in rendering PNG files output. You can use the arguments
plot = FALSE
to avoid PNG rendering on your cluster.
SVsignatures_exp <- deconvolution_fit_SV(vcf = SV.vcf,input_data = SV_input$mut_props,input_signatures = SV_denovo_sigs,sig_cols = SV_cols,resdir = '/home/fi1d18/new', plot=FALSE)
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