plot_peakGeneCor {FindIT2} | R Documentation |
plot_peakGeneCor
plot_peakGeneCor( mmAnnoCor, select_gene, addLine = TRUE, addFullInfo = TRUE, sigShow = c("pvalue", "padj", "qvalue") )
mmAnnoCor |
the annotated GRange object from peakGeneCor or enhancerPromoterCor |
select_gene |
a gene_id which you want to show |
addLine |
whether add cor line |
addFullInfo |
whether add full feature info on plot |
sigShow |
one of 'pvalue' 'padj' 'qvalue' |
ggplot2 object
if (require(TxDb.Athaliana.BioMart.plantsmart28)) { data("RNA_normCount") data("ATAC_normCount") Txdb <- TxDb.Athaliana.BioMart.plantsmart28 seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C")) peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2") peak_GR <- loadPeakFile(peak_path)[1:100] mmAnno <- mm_geneScan(peak_GR, Txdb) ATAC_colData <- data.frame( row.names = colnames(ATAC_normCount), type = gsub("_R[0-9]", "", colnames(ATAC_normCount)) ) integrate_replicates(ATAC_normCount, ATAC_colData) -> ATAC_normCount_merge RNA_colData <- data.frame( row.names = colnames(RNA_normCount), type = gsub("_R[0-9]", "", colnames(RNA_normCount)) ) integrate_replicates(RNA_normCount, RNA_colData) -> RNA_normCount_merge mmAnnoCor <- peakGeneCor( mmAnno = mmAnno, peakScoreMt = ATAC_normCount_merge, geneScoreMt = RNA_normCount_merge, parallel = FALSE ) plot_peakGeneCor(mmAnnoCor, select_gene = "AT5G01010") }