plot_heatmap: similarity matrix heatmap plotting

Description Usage Arguments Value Author(s) References Examples

View source: R/Plots.R

Description

plot heatmap of a disease similarity matrix

Usage

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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

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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)

dSimer documentation built on Nov. 17, 2017, 12:51 p.m.