## ----setup,echo=FALSE,results="hide"------------------------------------------ suppressPackageStartupMessages({ suppressMessages({ library(BiocStyle) library(HumanTranscriptomeCompendium) library(beeswarm) library(SummarizedExperiment) library(DT) }) }) ## ----lklo--------------------------------------------------------------------- library(HumanTranscriptomeCompendium) genelev = htx_load() genelev if (rhdf5client::check_hsds()) assay(genelev) ## ----lksi--------------------------------------------------------------------- sing = grep("single.cell", genelev$study_title, ignore.case=TRUE) length(sing) ## ----chkspec------------------------------------------------------------------ sa = genelev$study_accession[sing] sing2 = sing[-which(duplicated(sa))] length(sing2) datatable(as.data.frame(colData(genelev[,sing2])), options=list(lengthMenu=c(3,5,10,50,100))) ## ----lkchar------------------------------------------------------------------- bulk = genelev[,-sing] kpglio = grep("glioblastoma", bulk$study_title, ignore.case=TRUE) glioGene = bulk[,kpglio] glioGene ## ----lkmat-------------------------------------------------------------------- if (rhdf5client::check_hsds()) { beeswarm(unname(as.matrix(assay( glioGene["ENSG00000138413.13",1:100]))), pwcol=as.numeric(factor(glioGene$study_title[1:100])), ylab="IDH1 expression") legend(.6, 15000, legend=unique(glioGene$study_accession[1:100]), col=1:2, pch=c(1,1)) } ## ----dotx, eval=FALSE--------------------------------------------------------- # txlev = htx_load(genesOnly=FALSE) # txlev