xGSEAbarplot: Function to visualise GSEA results using a barplot

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xGSEAbarplot is supposed to visualise GSEA results using a barplot. It returns an object of class "ggplot".

Usage

xGSEAbarplot(
eGSEA,
top_num = 10,
displayBy = c("nes", "adjp", "fdr", "pvalue"),
FDR.cutoff = 0.05,
bar.label = TRUE,
bar.label.size = 3,
bar.color = "lightyellow-orange",
bar.width = 0.8,
wrap.width = NULL,
font.family = "sans",
signature = TRUE
)

Arguments

eGSEA	an object of class "eGSEA"
top_num	the number of the top terms (sorted according to FDR or adjusted p-values). If it is 'auto', only the significant terms (see below FDR.cutoff) will be displayed
displayBy	which statistics will be used for displaying. It can be "nes" for normalised enrichment score (by default), "adjp" or "fdr" for adjusted p value (or FDR), "pvalue" for p value
FDR.cutoff	FDR cutoff used to declare the significant terms. By default, it is set to 0.05. This option only works when setting top_num (see above) is 'auto'
bar.label	logical to indicate whether to label each bar with FDR. By default, it sets to true for bar labelling
bar.label.size	an integer specifying the bar labelling text size. By default, it sets to 3
bar.color	either NULL or fill color names ('lightyellow-orange' by default)
bar.width	bar width. By default, 80 data
wrap.width	a positive integer specifying wrap width of name
font.family	the font family for texts
signature	logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE showing which function is used to draw this graph

Value

an object of class "ggplot"

Note

none

See Also

xGSEAbarplot

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
bp <- xGSEAbarplot(eGSEA, top_num="auto", displayBy="nes")
#pdf(file="GSEA_barplot.pdf", height=6, width=12, compress=TRUE)
print(bp)
#dev.off()

## End(Not run)

Pi documentation built on Nov. 29, 2021, 3 p.m.