The goal of DGOplot is to perform enrichment analses on Disease Ontology and Gene Ontology and plot the result into a bar plot and a gene association network. Currently limited to HUMAN DATA ONLY.
You can install the latest version of DGOplot using:
require("devtools")
devtools::install_github("JoelleJee/DGOplot")
library("DGOplot")
Plotting DO and GO enrichment analyses two ways:
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The red and blue edges indicate DO and GO, respectively.
The author of the package is Yoonsun Jee. The functions available within this package include:
library("DGOplot")
lsf.str("package:DGOplot")
# double bar plot to show DO and GO enrichment analyses results
# DGObarplot : function (DGOResult, showCategory = 8, DOcol = c("red", "darksalmon"), GOcol = c("blue", "lightskyblue"), pAdjustCutoff = 0.05)
# draws a gene association network
# DGOnetplot : function (DGOResult, showCategory = 6, pAdjustCutoff = 0.05, cluster.strength = 10, GOcol = c("blue", "lightblue"),
# DOcol = c("red", "mistyrose"), termCol = "PuOr", geneCol = "honeydew3")
# computes GO and DO enrichment anlyses
# enrichDGO : function (gene, Gont = "MF", Dont = "DO", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2,
# minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
# shiny app GUI
# runDGOplot : function ()
The enrichDGO function performs the DO and GO enrichment analyses using functions from DOSE and clusterProfiler R packages. The DOSE R package is used for DO enrichment analysis while the clusterProfiler R package is used for GO enrichment analysis.
The DGObarplot function takes in the result from enrichDGO function and plots it into a double bar graph using ggplot2 R package.
The DGOnetPlot function uses the igraph R package and qgraph R package to graph a gene association network from the enrichDGO results.
This a simple example using the dataset provided from DOSE R package.
library(DGOplot)
## basic example code
data(geneList)
gene <- names(geneList)[abs(geneList) > 2]
x <- enrichDGO(gene, universe = names(geneList))
DGObarplot(x, showCategory=5)
DGOnetplot(x, showCategory=5)
Orgs.Hs.eg.db * Human genome data
ggnewscale, ggplot2, igraph * For bar plot and network plot
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