XGR (version 1.1.7)

xEnrichDotplot: Function to visualise enrichment results using dot-like plot

Description

xEnrichDotplot is supposed to visualise enrichment results using dot-like plot. It returns a ggplot2 object.

Usage

xEnrichDotplot(
eTerm,
FDR.cutoff = 0.05,
colors = c("pink", "red"),
y.scale = c("normal", "log"),
slim = NULL,
size.range = c(0.5, 3.5),
size.title = "Num of overlaps",
label.top = "auto",
label.direction.y = c("left", "right", "none"),
label.size = 2,
...
)

Arguments

eTerm

an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns (named as 'group','name','adjp','zscore','nOverlap')

FDR.cutoff

FDR cutoff used to declare the significant terms. By default, it is set to 0.05

colors

a 2-element vector for color-coded points. By default, it is c("pink","red"), responding to the insignificant and the significant

y.scale

how to transform the y scale. It can be "normal" for no transformation, and "log" for log-based transformation

slim

the minimum and maximum values for which sizes should be plotted

size.range

the range of actual node size

size.title

a character specifying the title for node sizing. By default it is 'Num of overlaps'

label.top

the number of the top terms (sorted according to adjp). Only the significant terms (see above FDR.cutoff) will be labelled

label.direction.y

how to align labels. It can be "none", "left" (align labels on the left edge) or "right" (align labels on the right edge). Only works for individual group

label.size

the size of the labellings

...

additional graphic parameters (such as size, color) used in ggrepel::geom_text_repel to control labels

Value

an object of class "ggplot"

See Also

xEnrichDotplot

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

gp <- xEnrichDotplot(eTerm, label.top=10)
# }