GO annotation E11.5
Ehsan Razmara Monash Uni
15/03/2022
library(patchwork)
library(enrichplot)## library("clusterProfiler")## clusterProfiler v3.18.1 For help: https://guangchuangyu.github.io/software/clusterProfiler
##
## If you use clusterProfiler in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.##
## Attaching package: 'clusterProfiler'## The following object is masked from 'package:stats':
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## filterlibrary("org.Mm.eg.db")## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics## Loading required package: parallel##
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## intersect, setdiff, setequal, unionlibrary(devtools)## Loading required package: usethispbmc <- readRDS("/mnt/nectar_volume/home/eraz0001/KELLY 2020/E11.5/Final_15_clusters.RDS")
pbmc.markers <- FindAllMarkers(pbmc, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25)## Calculating cluster DCh## Calculating cluster Osteocytes## Calculating cluster Osteoblast## Calculating cluster HtCh## Calculating cluster Osteoblasts## Calculating cluster Endothelial Cells## Calculating cluster Hoxd13+## Calculating cluster Chondrocytes## Calculating cluster Terminal HTCh## Calculating cluster Fibroblasts## Calculating cluster Immune cellstop100 <- pbmc.markers %>% group_by(cluster) %>% top_n(n = 100, wt = avg_log2FC)
top100pval <- subset(top100, rowSums(top100[5] < 0.05) > 0)df <- top100pval[,7:6]
dfsample <- split(df$gene,df$cluster)
length(dfsample)## [1] 11The number of dfsample can form the following steps; e.g., if we have “11,” we need to define eleven samples in the following.
dfsample$`DCh` = bitr(dfsample$`DCh`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$DCh, fromType = "SYMBOL", toType = "ENTREZID", : 7% of
## input gene IDs are fail to map...dfsample$`Osteocytes` = bitr(dfsample$`Osteocytes`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columnsdfsample$`Osteoblast` = bitr(dfsample$`Osteoblast`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$Osteoblast, fromType = "SYMBOL", toType = "ENTREZID", :
## 3.23% of input gene IDs are fail to map...dfsample$`HtCh` = bitr(dfsample$`HtCh`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$HtCh, fromType = "SYMBOL", toType = "ENTREZID", : 6% of
## input gene IDs are fail to map...dfsample$`Osteoblasts`= bitr(dfsample$`Osteoblasts`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$Osteoblasts, fromType = "SYMBOL", toType =
## "ENTREZID", : 3.03% of input gene IDs are fail to map...dfsample$`Endothelial Cells` = bitr(dfsample$`Endothelial Cells`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$`Endothelial Cells`, fromType = "SYMBOL", toType =
## "ENTREZID", : 2% of input gene IDs are fail to map...dfsample$`Hoxd13+` = bitr(dfsample$`Hoxd13+`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$`Hoxd13+`, fromType = "SYMBOL", toType = "ENTREZID", :
## 5% of input gene IDs are fail to map...dfsample$`Chondrocytes` = bitr(dfsample$`Chondrocytes`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$Chondrocytes, fromType = "SYMBOL", toType =
## "ENTREZID", : 3.03% of input gene IDs are fail to map...dfsample$`Terminal HTCh` = bitr(dfsample$`Terminal HTCh`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$`Terminal HTCh`, fromType = "SYMBOL", toType =
## "ENTREZID", : 2.04% of input gene IDs are fail to map...dfsample$`Fibroblasts` = bitr(dfsample$`Fibroblasts`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(dfsample$Fibroblasts, fromType = "SYMBOL", toType =
## "ENTREZID", : 1% of input gene IDs are fail to map...dfsample$`Immune cells` = bitr(dfsample$`Immune cells`, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Mm.eg.db")## 'select()' returned 1:1 mapping between keys and columnsThen the following step must be done:
genelist <- list("DCh" = dfsample$'DCh'$ENTREZID,
"Osteocytes" = dfsample$'Osteocytes'$ENTREZID,
"Osteoblast" = dfsample$'Osteoblast'$ENTREZID,
"HtCh" = dfsample$'HtCh'$ENTREZID,
"Osteoblasts" = dfsample$'Osteoblasts'$ENTREZID,
"Endothelial Cells" = dfsample$'Endothelial Cells'$ENTREZID,
"Hoxd13+" = dfsample$'Hoxd13+'$ENTREZID,
"Chondrocytes" = dfsample$'Chondrocytes'$ENTREZID,
"Terminal HTCh" = dfsample$'Terminal HTCh'$ENTREZID,
"Fibroblasts" = dfsample$'Fibroblasts'$ENTREZID,
"Immune cells" = dfsample$'Immune cells'$ENTREZID)GOclusterplot <- compareCluster(geneCluster = genelist, fun = "enrichGO", OrgDb = "org.Mm.eg.db")
dotplot(GOclusterplot)
GOclusterplot1 <- compareCluster(geneCluster = genelist, fun = "groupGO", OrgDb = "org.Mm.eg.db")
dotplot(GOclusterplot1)
#integrated plots
a1 <- pairwise_termsim(GOclusterplot)
emapplot(a1, showCategory = 20)
session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.2 (2020-06-22)
## os Ubuntu 20.04.3 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_AU.UTF-8
## ctype en_AU.UTF-8
## tz Australia/Melbourne
## date 2022-03-25
## pandoc 2.11.4 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)
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