Customizing and adding colorful and informative pathway tracks.

[erikagedvilaite]

Describe the issue

Hello, I would like to add colorful tracks underneath top 10 genes. Can I modify the pathway tracks to 1) show how the sample was sequenced (Illumina vs. IonTorrent vs. Both)? Would like to do that for top 10 genes for 100+ patients oncoplot

oncoplot(maf = laml, pathways = "auto", gene_mar = 8, fontSize = 0.6)

Session info
Run sessionInfo() and post the output below

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] VennDiagram_1.6.20  futile.logger_1.4.3 forcats_0.5.1       stringr_1.4.0       dplyr_1.0.5         purrr_0.3.4         readr_1.4.0         tidyr_1.1.3        
 [9] tibble_3.1.0        tidyverse_1.3.0     devtools_2.3.2      usethis_2.0.1       ggplot2_3.3.3       maftools_2.8.05    

loaded via a namespace (and not attached):
 [1] httr_1.4.2           pkgload_1.2.0        jsonlite_1.7.2       splines_3.6.3        modelr_0.1.8         assertthat_0.2.1     cellranger_1.1.0    
 [8] remotes_2.2.0        sessioninfo_1.1.1    pillar_1.6.0         backports_1.2.1      lattice_0.20-41      glue_1.4.2           digest_0.6.27       
[15] RColorBrewer_1.1-2   rvest_0.3.6          colorspace_2.0-0     Matrix_1.3-2         pkgconfig_2.0.3      broom_0.7.5          haven_2.3.1         
[22] scales_1.1.1         processx_3.4.5       farver_2.1.0         generics_0.1.0       ellipsis_0.3.1       cachem_1.0.4         withr_2.4.1         
[29] cli_2.4.0            survival_3.2-7       magrittr_2.0.1       crayon_1.4.1         readxl_1.3.1         memoise_2.0.0        ps_1.6.0            
[36] fs_1.5.0             fansi_0.4.2          xml2_1.3.2           pkgbuild_1.2.0       tools_3.6.3          data.table_1.14.0    prettyunits_1.1.1   
[43] hms_1.0.0            formatR_1.7          lifecycle_1.0.0      munsell_0.5.0        reprex_1.0.0         lambda.r_1.2.4       callr_3.5.1         
[50] compiler_3.6.3       rlang_0.4.10         rstudioapi_0.13      labeling_0.4.2       testthat_3.0.2       gtable_0.3.0         DBI_1.1.1           
[57] curl_4.3             R6_2.5.0             lubridate_1.7.10     knitr_1.31           fastmap_1.1.0        utf8_1.2.1           rprojroot_2.0.2     
[64] futile.options_1.0.1 desc_1.2.0           stringi_1.5.3        Rcpp_1.0.6           vctrs_0.3.7          dbplyr_2.1.0         tidyselect_1.1.0    
[71] xfun_0.21 

[PoisonAlien]

Hi,

Sure, you can add this info as a bottom annotation bar. Just create a table of sample names and sequencing platform, and pass it to the oncoplot command.

> head(seq_platform)
  Tumor_Sample_Barcode   Platform
1         TCGA-AB-2802   Illumina
2         TCGA-AB-2803    Complex
3         TCGA-AB-2804 IonTorrent
4         TCGA-AB-2805   Illumina
5         TCGA-AB-2806   Illumina
6         TCGA-AB-2807    Complex

oncoplot(
  maf = laml,
  pathways = "auto",
  annotationDat = seq_platform,
  clinicalFeatures = "Platform",
  sortByAnnotation = TRUE)