View source: R/plot-KEGG-map.R
plotKEGGMap | R Documentation |
This function plots KEGG map with DE genes.
plotKEGGMap(
DEResults,
KEGGPathwayID,
statistic = "logFC",
useFDR = TRUE,
pThreshold = 0.05,
statLimit = 3
)
DEResults |
A named list of data frame of DE analysis results. The columns of each data frame should be at least ID, logFC, p.value and pFDR. |
KEGGPathwayID |
The KEGG pathway ID. |
statistic |
The column name of the statistic used to plot the DE genes. If statistic is p.value or pFDR, all genes are colored. Otherwise, only DE genes are colored. |
useFDR |
If TRUE, DE genes are selected based on pFDR, otherwise p.value. |
pThreshold |
The p-value threshold to select DE genes. Only used when statistic is not p.value or pFDR. |
statLimit |
The absolute value of the statistic to color the DE genes. If statistic is p.value or pFDR, this parameter is the limit of -log10(p-value). Otherwise, this parameter is the limit of the absolute value of the statistic. |
A list with the following elements:
plot: A ggplot object of the KEGG map.
width: The width of the KEGG map.
height: The height of the KEGG map.
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)
)
plotObj <- RCPA::plotKEGGMap(DEResults, "hsa05010", stat = "logFC", pThreshold = 1, statLimit = 1)
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