Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 7.2,
fig.height = 4.3,
fig.retina = 2
)
## ---- message = FALSE, warning = FALSE----------------------------------------
# Load all the packages:
library(data.table)
library(ggplot2)
library(dplyr)
library(stringr)
library(clusterProfiler)
library(DOSE)
library(org.Hs.eg.db)
library(aPEAR)
data(geneList)
# Perform enrichment using clusterProfiler
set.seed(42)
enrich <- gseGO(geneList, OrgDb = org.Hs.eg.db, ont = 'CC')
## ---- fig.height = 6----------------------------------------------------------
set.seed(654824)
enrichmentNetwork(enrich@result)
## ---- include = FALSE, echo = FALSE-------------------------------------------
enrichmentData <- enrich@result %>%
as.data.table() %>%
.[ 1:5 ] %>%
.[ , list(Description, pathwayGenes = core_enrichment, NES, Size = setSize) ] %>%
.[ , pathwayGenes := str_trunc(pathwayGenes, 20) ]
## -----------------------------------------------------------------------------
enrichmentData[ 1:5 ]
## ---- include = FALSE, echo = FALSE-------------------------------------------
enrichmentData <- enrich@result %>%
as.data.table() %>%
.[ , list(Description, pathwayGenes = core_enrichment, NES, Size = setSize) ]
## -----------------------------------------------------------------------------
p <- enrichmentNetwork(enrichmentData, colorBy = 'NES', nodeSize = 'Size', verbose = TRUE)
## -----------------------------------------------------------------------------
set.seed(348934)
enrichmentNetwork(enrich@result, colorBy = 'pvalue', colorType = 'pval', pCutoff = -5)
## -----------------------------------------------------------------------------
clusters <- findPathClusters(enrich@result, cluster = 'hier', minClusterSize = 6)
clusters$clusters[ 1:5 ]
pathways <- clusters$clusters[ 1:5, Pathway ]
clusters$similarity[ pathways, pathways ]
## -----------------------------------------------------------------------------
set.seed(238923)
plotPathClusters(
enrichment = enrich@result,
sim = clusters$similarity,
clusters = clusters$clusters,
fontSize = 4,
outerCutoff = 0.01, # Decrease cutoff between clusters and show some connections
drawEllipses = TRUE
)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.