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

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

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"

Note

none

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)

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.