Customizing and adding colorful and informative pathway tracks. #742
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erikagedvilaite
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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) |
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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 belowBeta Was this translation helpful? Give feedback.
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