plotVennDE | R Documentation |
Plot a Venn diagram from multiple DE Analysis results.
plotVennDE(
DEResults,
pThreshold = 0.05,
useFDR = TRUE,
stat = "logFC",
statThreshold = 0,
topToList = 10
)
DEResults |
A list of data frames with the results of DE analysis. |
pThreshold |
The p-value threshold to determine if a gene is differentially expressed. |
useFDR |
Use the FDR adjusted p-value instead of the raw p-value. |
stat |
The additional statistics column to use for filtering differentially expressed genes. |
statThreshold |
The absolute value of the statistic threshold to use for filtering differentially expressed genes. Default is 0, which means no filtering. |
topToList |
The number of common DE genes that are used to annotate the plot |
A ggplot2 object.
library(RCPA)
library(SummarizedExperiment)
affyDEExperiment <- loadData("affyDEExperiment")
agilDEExperiment <- loadData("agilDEExperiment")
RNASeqDEExperiment <- loadData("RNASeqDEExperiment")
DEResults <- list(
"Affymetrix - GSE5281" = rowData(affyDEExperiment),
"Agilent - GSE61196" = rowData(agilDEExperiment),
"RNASeq - GSE153873" = rowData(RNASeqDEExperiment)
)
DEResultUps <- lapply(DEResults, function(df) df[!is.na(df$logFC) & df$logFC > 0, ])
DEResultDowns <- lapply(DEResults, function(df) df[!is.na(df$logFC) & df$logFC < 0, ])
if (require("ggvenn", quietly = TRUE)){
p1 <- RCPA::plotVennDE(DEResults) +
ggplot2::ggtitle("All DE Genes")
p2 <- RCPA::plotVennDE(DEResultUps) +
ggplot2::ggtitle("Up-regulated DE Genes")
p3 <- RCPA::plotVennDE(DEResultDowns) +
ggplot2::ggtitle("Down-regulated DE Genes")
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.