## ----lkd---------------------------------------------------------------------- suppressPackageStartupMessages({ library(BiocOncoTK) library(ggplot2) }) molpo_CDS ## ----make2a------------------------------------------------------------------- library(SummarizedExperiment) sev = apply(assay(molpo_CDS),1,sum) litass = assay(molpo_CDS[names(sort(sev,decreasing=TRUE)[1:50]),]) dd = data.frame(t(litass), tumor=molpo_CDS$tumor_type) library(dplyr) library(magrittr) names(dd) = gsub("_.*", "", names(dd)) library(reshape2) ddm = melt(dd) names(ddm)[2] = "gene" names(ddm)[3] = "msi_cds" if (.Platform$OS.type != "windows") { ggplot(ddm %>% filter(msi_cds>0), aes(x=gene,fill=tumor)) + geom_bar() + theme(axis.text.x = element_text(angle = 90, hjust = 1)) } ## ----make3a------------------------------------------------------------------- lit = molpo_WGS[1,molpo_WGS$tumor_type %in% c("UCEC", "BRCA", "KIRP")] myd = data.frame(totmsi=t(assay(lit[1,])), tumor=lit$tumor_type) ss = split(myd, myd$tumor) ss[[1]]$x = 1:nrow(ss[[1]]) ss[[2]]$x = 1:nrow(ss[[2]]) ss[[3]]$x = 1:nrow(ss[[3]]) ssd = do.call(rbind,ss) if (.Platform$OS.type != "windows") { ggplot(ssd, aes(y=Total_number_MSI_events+1,x=x)) + geom_point() + facet_grid(.~tumor, scales="free_x")+ scale_y_log10() } ## ----getms-------------------------------------------------------------------- data(MSIsensor.10k) data(patient_to_tumor_code) names(MSIsensor.10k)[1] = "patient_barcode" mm = merge(MSIsensor.10k, patient_to_tumor_code) if (.Platform$OS.type != "windows") { ggplot(mm, aes(y=MSIsensor.score+1, x=tumor_code)) + geom_boxplot() + coord_flip() + scale_y_log10() }