library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
txdb1=TxDb.Hsapiens.UCSC.hg38.knownGene
files <- getSampleFiles()
peakAnnoList1 <- lapply(files, annotatePeak,
TxDb=txdb1,tssRegion=c(-3000, 3000))
peakAnnoList <- lapply(files, annotatePeak,
TxDb=txdb,tssRegion=c(-3000, 3000))
## get the first barplot with TxDb.Hsapiens.UCSC.hg19.knownGene
plotAnnoBar(peakAnnoList)
## get the second barplot with TxDb.Hsapiens.UCSC.hg38.knownGene
plotAnnoBar(peakAnnoList1)
using different kinds of txdb files will return different amounts of categories which will lead to different color scheme.
This update is to simply change the color scheme which may sacrifice the diversity of color. But since the color is immoblized we can see the difference between different txdb files annotating the same peaks.
## using new color scheme to get the first barplot
plotAnnoBar(peakAnnoList)
## using new color scheme to get the second barplot
plotAnnoBar(peakAnnoList1)
As it shown, we can clearly see the difference between txdb files.
This pull request is to change color scheme of
plotAnnoBar()
. The issues are mentioned in https://github.com/YuLab-SMU/ChIPseeker/issues/83#issuecomment-481520275 and https://github.com/YuLab-SMU/ChIPseeker/issues/83#issuecomment-848871641. Using different kinds of txdb files will return different amount of categories. for example:using different kinds of txdb files will return different amounts of categories which will lead to different color scheme.
This update is to simply change the color scheme which may sacrifice the diversity of color. But since the color is immoblized we can see the difference between different txdb files annotating the same peaks.
As it shown, we can clearly see the difference between txdb files.