Description Usage Arguments Author(s) Examples
FastGOplot give fast way to draw GO series plot like barplot/dotplot/emapplot,Cnetplot and goplot for a enrichGO object based on clusterProfiler package.
1 2 3 4 |
genes |
a character of gene id. |
geneList |
a numeric with id names.For example,logFoldChang with ENSEMBL id names.Note that the names of |
default.universe |
whether to use default universe.If |
classlevel |
Default is 2.I had tested that 2:7 was still available.If many levels is set,the process is time-consuming |
OrgDb |
OrgDb dataset.If NULL,use "org.Hs.eg.db" |
keyType |
the type of gene.Support automatically test |
pAdjustMethod |
the mathod of pvalue adjustment |
pvalueCutoff |
a list of pvalue adjust method for |
qvalueCutoff |
cutoff of q value |
cnet.showCategory |
the number of showed cluster at cnetplot |
verbose |
LuckyVerbose gseplot running message or not |
save.path |
the sub path of saved files |
names |
the main path and part names of saved files |
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | library(lucky)
need <- c("clusterProfiler","org.Hs.eg.db");Plus.library(need)
data(geneList, package = "DOSE")
data(geneList, package='DOSE')
universe <- unique(as.character(common.annot$ENTREZID))
system.time(
l <- FastGO(genes,
geneList,
classlevel = 2:2,
OrgDb = NULL,
keyType = NULL,
pAdjustMethod = "BH",
pvalueCutoff = list(
gseGO = 0.05,
enrichGO = 0.05),
qvalueCutoff = 0.05,
cnet.showCategory = 5,
save.path = "GO",
names = "love")
)
## enhanced plot
g <- enrichplot::cnetplot(goList$GOEnrichment$BP,
showCategory=10,
colorEdge=T,
node_label=T,
circular = F)
g1 <- g + theme(legend.text = element_text(face = "bold",size = 12))
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