Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update KEGG API #540

Merged
merged 5 commits into from
Mar 1, 2023
Merged

update KEGG API #540

Show file tree
Hide file tree
Changes from 4 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
10c29b7
Merge pull request #22 from YuLab-SMU/master
huerqiang Oct 29, 2022
a379dd5
Merge pull request #23 from YuLab-SMU/master
huerqiang Mar 1, 2023
d2a1e70
update KEGG API
huerqiang Mar 1, 2023
7bee9dc
Update DESCRIPTION
GuangchuangYu Mar 1, 2023
a171052
Update NEWS.md
GuangchuangYu Mar 1, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: clusterProfiler
Type: Package
Title: A universal enrichment tool for interpreting omics data
Version: 4.7.0
Version: 4.7.1
Authors@R: c(
person(given = "Guangchuang", family = "Yu", email = "[email protected]", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
person(given = "Li-Gen", family = "Wang", email = "[email protected]", role = "ctb"),
Expand Down
2 changes: 2 additions & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ TODO:


-->
# clusterProfiler 4.7.0.991
+ update KEGG api (2023-03-01, Wed)

# clusterProfiler 4.5.3

Expand Down
7 changes: 4 additions & 3 deletions R/enrichKEGG.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -176,8 +176,8 @@ download.KEGG.Path <- function(species) {
keggpathid2extid.df[,1] %<>% gsub("[^:]+:", "", .)
keggpathid2extid.df[,2] %<>% gsub("[^:]+:", "", .)

keggpathid2name.df <- kegg_list("pathway")
keggpathid2name.df[,1] %<>% gsub("path:map", species, .)
keggpathid2name.df <- kegg_list("pathway", species)
# keggpathid2name.df[,1] %<>% gsub("path:map", species, .)

## if 'species="ko"', ko and map path are duplicated, only keep ko path.
##
Expand All @@ -204,7 +204,8 @@ download.KEGG.Module <- function(species) {
keggmodule2extid.df[,2] %<>% gsub("[^:]+:", "", .)

keggmodule2name.df <- kegg_list("module")
keggmodule2name.df[,1] %<>% gsub("md:", "", .)
# now module do not nedd sub 'md:'
# keggmodule2name.df[,1] %<>% gsub("md:", "", .)
return(list(KEGGPATHID2EXTID=keggmodule2extid.df,
KEGGPATHID2NAME =keggmodule2name.df))
}
Expand Down
2 changes: 1 addition & 1 deletion R/gson.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -143,7 +143,7 @@ gson_KEGG_mapper = function(file,
}

if (type == "pathway"){
all_pathway = kegg_list("pathway")
all_pathway = kegg_list("pathway", species)
colnames(all_pathway) = c("pathway","pathway_name")
all_pathway %<>%
dplyr::mutate_at(.vars = "pathway", .funs = "remove_db_prefix")
Expand Down
10 changes: 8 additions & 2 deletions R/kegg-utilities.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -140,8 +140,14 @@ kegg_link <- function(target_db, source_db) {
}


kegg_list <- function(db) {
url <- paste0("https://rest.kegg.jp/list/", db, collapse="")
kegg_list <- function(db, species = NULL) {
if (db == "pathway") {
url <- paste("https://rest.kegg.jp/list", db, species, sep="/")
} else {
## module do not need species
url <- paste("https://rest.kegg.jp/list", db, sep="/")
}

kegg_rest(url)
}

Expand Down