XGR (version 1.1.7)

xEnrichChord: 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

See Also

xEnrichChord

Examples

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

xEnrichChord(eTerm)
# }