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Add species specification, complete documentation, and fix tempdir problem in double_enrich function #12

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Add species specification, complete documentation, and fix tempdir problem in double_enrich function #12

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b51ade1
feat: add species specification feature to double_enrich() function
kusurin Dec 14, 2024
47108e2
docs: complete documentation for quick_enrich() and double_enrich() f…
kusurin Dec 14, 2024
976ff4c
fix: avoid `double_enrich()` reading first result
kusurin Dec 14, 2024
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11 changes: 8 additions & 3 deletions R/7_quick_double_enrich.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
##' @param genes a gene symbol or entrizid vector
##' @param kkgo_file Rdata filename for kegg and go result
##' @param destdir destdir to save kkgofile
##' @param species species for enrichment analysis, e.g. "human","mouse","rat"
##' @inheritParams trans_exp_new
##' @return enrichment results and dotplots
##' @author Xiaojie Sun
Expand Down Expand Up @@ -112,6 +113,7 @@ quick_enrich <- function(genes,
##' @param deg a data.frame contains at least two columns:"ENTREZID" and "change"
##' @param n how many terms will you perform for up and down genes respectively
##' @param color color for bar plot
##' @param species species for enrichment analysis, e.g. "human","mouse","rat"
##' @return a list with kegg and go bar plot according to up and down genes enrichment result.
##' @author Xiaojie Sun
##' @importFrom stringr str_to_lower
Expand Down Expand Up @@ -146,14 +148,17 @@ quick_enrich <- function(genes,
##' @seealso
##' \code{\link{quick_enrich}}

double_enrich <- function(deg,n = 10,color = c("#2874C5", "#f87669")){
double_enrich <- function(deg,n = 10,color = c("#2874C5", "#f87669"), species = "human"){

if(!requireNamespace("labeling",quietly = TRUE)) {
stop("Package \"labeling\" needed for this function to work. Please install it byby install.packages('labeling')",call. = FALSE)
}
deg$change = str_to_lower(deg$change)
up = quick_enrich(deg$ENTREZID[deg$change=="up"],"up.rdata",destdir = tempdir())
down = quick_enrich(deg$ENTREZID[deg$change=="down"],"down.rdata",destdir = tempdir())
timestamp <- format(Sys.time(), "%Y%m%d%H%M%S")
temp_dir <- file.path(tempdir(), timestamp)
dir.create(temp_dir, recursive = TRUE)
up = quick_enrich(deg$ENTREZID[deg$change=="up"], "up.rdata", destdir = temp_dir, species = species)
down = quick_enrich(deg$ENTREZID[deg$change=="down"], "down.rdata", destdir = temp_dir, species = species)
if(!is.null(up$kk) & !is.null(down$kk) &!is.null(up$go) &!is.null(up$go)){
up$kk@result = mutate(up$kk@result,change = "up")
down$kk@result = mutate(down$kk@result,change = "down")
Expand Down