plot_heatmap: similarity matrix heatmap plotting

In PengNi/dSimer: Integration of Disease Similarity Methods

Description

plot heatmap of a disease similarity matrix

Usage

plot_heatmap(simmat, xlab = "", ylab = "", color.low = "white",
  color.high = "red", labs = TRUE, digits = 2, labs.size = 3,
  font.size = 14)

Arguments

simmat	a similarity matrix
xlab	xlab
ylab	ylab
color.low	color of low value
color.high	color of high value
labs	logical, add text label or not
digits	round digit numbers
labs.size	lable size
font.size	font size

Value

a ggplot object

Author(s)

Peng Ni, Min Li

References

Yu G, Wang L G, Yan G R, et al. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis[J]. Bioinformatics, 2015, 31(4): 608-609.

Examples

data(d2g_separation)
data(interactome)

graph_interactome<-graph.data.frame(interactome,directed=FALSE)
ds<-c("myocardial ischemia","myocardial infarction","coronary artery disease",
 "cerebrovascular disorders","arthritis, rheumatoid","diabetes mellitus, type 1",
 "autoimmune diseases of the nervous system","demyelinating autoimmune diseases, cns",
 "respiratory hypersensitivity","asthma","retinitis pigmentosa",
 "retinal degeneration","macular degeneration")
 
sep<-Separation(ds,ds,d2g_separation,graph_interactome)
sim<-Separation2Similarity(sep)
plot_heatmap(sim)

PengNi/dSimer documentation built on May 8, 2019, 1:28 a.m.