Extract TSB order from oncoplot

[GeroKn]

Hi all,

I was wondering whether there is a way to extract the order of samples (and of genes) from the oncoplot?

Best and thanks in advance!
Gero

[PoisonAlien]

Hi,
oncoplot function silently returns the underlying matrix used for the plotting. You can capture it in a variable for further processing. I hope this helps.

[PoisonAlien]

Hi,
It returns the complete matrix in the order used in the oncoplot matrix.

laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools") #MAF file
laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #clinical data
laml = read.maf(maf = laml.maf, clinicalData = laml.clin)

> l = maftools::oncoplot(maf = laml)

# row order (gene names)
> rownames(l$oncomatrix)
 [1] "FLT3"   "DNMT3A" "NPM1"   "IDH2"   "IDH1"   "TET2"   "RUNX1"  "NRAS"   "TP53"  
[10] "CEBPA"  "WT1"    "PTPN11" "KIT"    "KRAS"   "U2AF1"  "SMC3"   "PHF6"   "SMC1A" 
[19] "STAG2"  "TTN"

# column order (sample names)
> colnames(l$oncomatrix) |> head()
[1] "TCGA-AB-2945" "TCGA-AB-2965" "TCGA-AB-2993" "TCGA-AB-2825" "TCGA-AB-2869"
[6] "TCGA-AB-2947"

Hope the helps.

[GeroKn]

Hi,

This is strange, it doesn't for me:

library(maftools)
laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools") #MAF file
laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #clinical data
laml = read.maf(maf = laml.maf, clinicalData = laml.clin)

> l = maftools::oncoplot(maf = laml)
> class(l)
[1] "character"

> l$oncomatrix
Error in l$oncomatrix : $ operator is invalid for atomic vectors

> l[1:5]
[1] "TCGA-AB-2945" "TCGA-AB-2965" "TCGA-AB-2993" "TCGA-AB-2825" "TCGA-AB-2869"

My best guess is that this must be some version problem, however I'm at R 4.4 and maftools is at 2.22.10, which should be the most recent:

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] maftools_2.22.10   data.table_1.16.4  pals_1.9           pheatmap_1.0.12    gplots_3.2.0       RColorBrewer_1.1-3
[7] dplyr_1.1.4        tidyr_1.3.1       

loaded via a namespace (and not attached):
 [1] Matrix_1.7-2        gtable_0.3.6        BiocManager_1.30.25 compiler_4.4.1      maps_3.4.2.1       
 [6] gtools_3.9.5        tidyselect_1.2.1    bitops_1.0-9        dichromat_2.0-0.1   splines_4.4.1      
[11] scales_1.3.0        lattice_0.22-6      DNAcopy_1.78.0      R6_2.6.0            generics_0.1.3     
[16] curl_6.2.0          mapproj_1.2.11      tibble_3.2.1        munsell_0.5.1       pillar_1.10.1      
[21] R.utils_2.12.3      rlang_1.1.5         caTools_1.18.3      cli_3.6.3           withr_3.0.2        
[26] magrittr_2.0.3      grid_4.4.1          rstudioapi_0.17.1   remotes_2.5.0       lifecycle_1.0.4    
[31] R.oo_1.27.0         R.methodsS3_1.8.2   vctrs_0.6.5         KernSmooth_2.23-26  glue_1.8.0         
[36] survival_3.8-3      hash_2.2.6.3        colorspace_2.1-1    purrr_1.0.4         tools_4.4.1        
[41] pkgconfig_2.0.3 

Do you see an issue here?

[PoisonAlien]

Hi,

Your version is correct. I have tested it on multiple machines and I can not seem to reprodcue your results. It should return the list of matrix, color codings, etc. I cant guess of any reason why this would happen.

[GeroKn]

Hi,

It is working now. I did some updating before the previous post. It's possible that something wasn't reloaded. Anyway, after a complete restart of R everything worked. Unfortunately I don't know the version numbers I had before updating, but my best guess is that there was something outdated version still loaded and that was resolved after the restart.

Anyway, thank you very much for your immediate help and apologies for the trouble.

Best!
Gero

[PoisonAlien]

No problems at all. Glad you solved it.