mycol

[ekfchan]

Hi Jay & Palimpsest Dev Team,

I think palimpsest_DissectSigs() & palimpsest_clonalitySigsCompare() are expecting the variable mycol to be in the global environment as it is not defined within the functions ...?

Thanks.

[jayendrashinde91]

Hi, Thanks for reaching out. I would like to redirect you to a previous issue: https://github.com/FunGeST/Palimpsest/issues/10

The variable mycol is defined early in the mutational signature analysis and consistently followed throughout the example script for further analysis including palimpsest_DissectSigs() & palimpsest_clonalitySigsCompare(). Hope this helps in clarifying your doubt.

Best, Jay

[ekfchan]

Hi Jay, shouldn't mycol be a local variable within these two functions rather than having the functions search for them globally? Thanks.

[jayendrashinde91]

I am not sure I completely understand the problem you are facing here. The user is, of course, free to define mycol at any step of the script. The RUNNING_PALIMPSEST_EXAMPLE script follows the logic of performing complete analysis on a given dataset. We start with defining mycol representing each signature extracted at the beginning and being consistent with mycol variable throughout the further analysis and visualizations. Best,

Jay

[ekfchan]

Hi Jay, Sorry I wasn't clear. I am not following the RUNNING_PALIMPSEST_EXAMPLE script. As such, I never defined mycol. So when I called palimpsest_DissectSigs, it failed because mycol was not defined. More specifically, palimpsest_DissectSigs takes the following arguments (per your code https://github.com/FunGeST/Palimpsest/blob/master/R/palimpsest_plotting.R):

palimpsest_DissectSigs <- function(vcf=NULL,
                                   signatures_exp_clonal=NULL,
                                   signatures_exp_subclonal=NULL,
                                   sig_cols=NULL,
                                   resdir=NULL)

As such, I called the function as follows, where cosmiccol is a named vector of colours and mysigs is a vector of signature names:

> palimpsest_DissectSigs(vcf=my.vcf, signatures_exp_clonal = clonal.sig, signatures_exp_subclonal = subclonal.sig, sig_cols = cosmiccol[mysigs], resdir=resdir.)

> cosmiccol
 Signature.1  Signature.2  Signature.3  Signature.4  Signature.5  Signature.6  Signature.7 
   "#8DD3C7"    "#984EA3"    "#7FC97F"    "#FB8072"    "#D95F02"    "#F1E2CC"    "#FB9A99" 
 Signature.8  Signature.9 Signature.10 Signature.11 Signature.12 Signature.13 Signature.14 
   "#A65628"    "#FFF2AE"    "#CAB2D6"    "#F0027F"    "#1F78B4"    "#4DAF4A"    "#BEAED4" 
Signature.15 Signature.16 Signature.17 Signature.18 Signature.19 Signature.20 Signature.21 
   "#CCCCCC"    "#E31A1C"    "#FDB462"    "#E6F5C9"    "#D9D9D9"    "#666666"    "#FFD92F" 
Signature.22 Signature.23 Signature.24 Signature.25 Signature.26 Signature.27 Signature.28 
   "#E41A1C"    "#377EB8"    "#386CB0"    "#FFFFB3"    "#E5D8BD"    "#A6CEE3"    "#FFFFCC" 
Signature.29 Signature.30 
   "#B15928"    "#FDDAEC" 
> mysigs
 [1] "Signature.1"  "Signature.3"  "Signature.5"  "Signature.8"  "Signature.9"  "Signature.12"
 [7] "Signature.16" "Signature.17" "Signature.18" "Signature.30"

As you can see, I have supplied a value to the sig_cols argument. But in the code, this argument is not used. Instead, it uses the default value to sig_col which is mycol.

barplot(ptt,col=mycol[rownames(mat)],las=1,ylab="Proportion of mutations",names.arg=c(paste("clonal\nn=",nearly,sep=""),paste("subclonal\nn=",nlate,sep="")),xlim=c(0,4.5))
title(paste("p=",chisq.test(mat)$p.value))
legend("topright",legend=rownames(mat),fill=mycol[rownames(mat)],bty="n")

Does this make sense?

[jayendrashinde91]

Thanks so much for bringing this to our notice. We have pushed the quick fix and replaced the couple of lines of code with sig_cols and the issue should be sorted now.

Best, Jay

[ekfchan]

Yup, that fixed it. Thanks!

[ekfchan]

Oh, actually, the issue is still present in palimpsest_clonalitySigsCompare(), specifically in the line:

legend(-3.8,-1.35,legend = names(mycol),ncol = 5,fill=mycol,border = mycol,bty = "n",cex=1)

[jayendrashinde91]

Thanks. It should be fixed now.