xGSEAbarplot | R Documentation |
xGSEAbarplot
is supposed to visualise GSEA results using a
barplot. It returns an object of class "ggplot".
xGSEAbarplot(eGSEA, top_num = 10, displayBy = c("nes", "adjp", "fdr", "pvalue"), FDR.cutoff = 0.05, bar.label = TRUE, bar.label.size = 3, wrap.width = NULL, signature = TRUE)
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 |
wrap.width |
a positive integer specifying wrap width of name |
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 |
an object of class "ggplot"
none
xPierGSEA
## Not run: # Load the library library(Pi) ## End(Not run) RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev" ## 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)