plot_Enrich: Plot results of FET/GSEA enrichment analysis

In WTaoUMC/RegEnrich: Gene regulator enrichment analysis

Description

Plot FET/GSEA enrichment results. If the FET method is applied, the top 'showCategory' regulator will be plotted. If the GSEA method is applied, the GSEA graph of regulator 'reg' will be plotted.

Usage

plot_Enrich(object, ...)

## S4 method for signature 'RegenrichSet'
plot_Enrich(
  object,
  reg = NULL,
  showCategory = 20,
  regDescription = NULL,
  font.size = 12
)

Arguments

object	a RegenrichSet object.
...	other parameters.
reg	The regulator to plot. This only works when the GSEA enrichment method has used.
showCategory	the number of regulator to plot.
regDescription	NULL or a two-column data frame, in which first column is the regulator IDs (for example ENSEMBL IDs), and the second column is the description of regulators (for example gene name). Default is NULL, meaning both columns are the same regulator names/IDs in the network.
font.size	font size of axis labels and axis tick mark labels, default is 12.

Value

a ggplot object of plotting FET or GSEA enrichment result.

Examples

# library(RegEnrich)
data("Lyme_GSE63085")
data("TFs")

data = log2(Lyme_GSE63085$FPKM + 1)
colData = Lyme_GSE63085$sampleInfo

# Take first 2000 rows for example
data1 = data[seq(2000), ]

design = model.matrix(~0 + patientID + week, data = colData)
object = RegenrichSet(expr = data1,
                      colData = colData,
                      method = "limma", minMeanExpr = 0,
                      design = design,
                      contrast = c(rep(0, ncol(design) - 1), 1),
                      networkConstruction = "COEN",
                      enrichTest = "FET")
# Differential expression analysis
object = regenrich_diffExpr(object)
# Network inference using "COEN" method
object = regenrich_network(object)
# Enrichment analysis by Fisher's exact test (FET)
object = regenrich_enrich(object)
# plot
plot_Enrich(object)

# Enrichment analysis by Fisher's exact test (FET)
object = regenrich_enrich(object, enrichTest = "GSEA")
# plot
plot_Enrich(object)

WTaoUMC/RegEnrich documentation built on Aug. 4, 2021, 4:11 p.m.