# #——lkd ---------------------------------------------------------------------- suppressPackageStartupMessages({库(BiocOncoTK)库(ggplot2)}) molpo_CDS # #——make2a ------------------------------------------------------------------- 库(SummarizedExperiment)签订=应用(化验(molpo_CDS), 1,总和)立特=测定(molpo_CDS[名称(排序(塞,减少= TRUE) (1:50)),]) dd = data.frame (t(立特),肿瘤= molpo_CDS tumor_type美元)图书馆(dplyr)图书馆(magrittr)名称(dd) = gsub(“_。*"， ""， names(dd)) library(reshape2) ddm = melt(dd) names(ddm)[2] = "gene" names(ddm)[3] = "msi_cds" if (. platform $OS. txt)Type != "windows") {ggplot(ddm %>% filter(msi_cds>0)， aes(x=gene,fill=tumor)) + geom_bar() + theme(axis.text. text. filter)x = element_text(角= 90,hjust = 1 )) } ## ---- make3a ------------------------------------------------------------------- 点燃= molpo_WGS [1, molpo_WGS tumor_type % % c(“UCEC”、“BRCA”,“KIRP”)]myd = data.frame (totmsi = t(化验([1])点燃),肿瘤=点燃tumor_type美元)党卫军=分裂(myd, myd肿瘤美元)党卫军[[1]]$ x = 1: nrow党卫军(ss [[1]]) [[2]] $ x = 1: nrow党卫军(ss [[2]]) [[3]] $ x = 1: nrow (ss [[3]]) ssd = do.call (rbind ss)如果(.Platform $ OS。type != "windows") {ggplot(ssd, aes(y=Total_number_MSI_events+1,x=x)) + geom_point() + facet_grid(。~肿瘤,鳞片=“free_x”)+ scale_y_log10 () } ## ---- getms -------------------------------------------------------------------- 数据(MSIsensor.10k)数据(patient_to_tumor_code)名称(MSIsensor.10k) [1] = " patient_barcode "毫米= (MSIsensor合并。if (. platform $OS. code)type != "windows") {ggplot(mm, aes(y= mssensor . type != "windows")Score +1, x=tumor_code)) + geom_boxplot() + coord_flip() + scale_y_log10()}