xEnrichChord: Function to visualise enrichment results using a chord plot

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

Function to visualise enrichment results using a chord plot

Description

xEnrichChord is supposed to visualise enrichment results using a chord plot. The thickness of links is proportional to the enrichment Z-scores. Particularly useful for multiple groups and/or ontologies. The left-half part sorted by the input groups (anti-clockwise), and the right-half part sorted first by the input ontologies and then by the number of links within an ontology (clockwise).

Usage

xEnrichChord(
eTerm,
top_num = 5,
FDR.cutoff = 0.05,
colormap.group = "ggplot2",
colormap.ontology = NULL,
wrap.width = NULL,
text.size = 0.6,
legend = NULL,
vline = F,
...
)

Arguments

eTerm	an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having all these columns (named as 'group','ontology','name','adjp','zscore')
top_num	the number of the top terms (sorted according to adjp). For the eTerm object, if it is 'auto' (for eTerm), only the significant terms (see below FDR.cutoff) will be displayed
FDR.cutoff	FDR cutoff used to declare the significant terms. By default, it is set to 0.05
colormap.group	short name for the group sector colormap
colormap.ontology	short name for the ontology sector colormap
wrap.width	a positive integer specifying wrap width of labellings
text.size	the text size of the labelings. By default, it is 0.6
legend	logical to indicate whether to show the legend. If NULL, automatically determined. For the group sector, the legends shown on the bottom-left corner. For the ontology sector, the legends shown on the bottom-right corner
vline	logical to indicate whether to vertically put a line seperating two symmetric parts of sectors
...	additional graphic parameters (such as big.gap=15, small.gap=1.5) used in circlize::chordDiagram

Value

a data frame used for visualisation

Note

none

See Also

xEnrichChord

Examples

## Not run: 
# Load the library
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

xEnrichChord(eTerm)

## End(Not run)

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