dpgsea

DESCRIPTION

@@ -6,7 +6,7 @@ License: GPL-3
 Description: Analysis toolkit for intra-species diversity from metagenomics.
 Authors@R: person("Noriaki", "Sato", email = "nori@hgc.jp", role = c("cre", "aut"))
 Depends: ggplot2, ggstar, ggraph, igraph
-Imports: GetoptLong, BiocFileCache, RCurl, igraph, vegan, methods, data.table, phangorn, RColorBrewer, ggtree, circlize, ComplexHeatmap, ggkegg, ape, dplyr, exactRankTests, ggblend, ggh4x, scales, tidygraph, ggplotify, ggtreeExtra, ggnewscale, scico
+Imports: GetoptLong, BiocFileCache, RCurl, igraph, vegan, methods, data.table, phangorn, RColorBrewer, ggtree, circlize, ComplexHeatmap, ggkegg, ape, dplyr, exactRankTests, ggblend, ggh4x, scales, tidygraph, ggplotify, ggtreeExtra, ggnewscale, scico, MKmisc
 Suggests: simplifyEnrichment, stringr, tidyr, Boruta, knitr, ggrepel
 RoxygenNote: 7.3.0
 VignetteBuilder: knitr

R/doGSEA.R

@@ -6,6 +6,7 @@
 #' 
 #' @param zeroPerc genes >= the percentage of count zero sample will be excluded.
 #' Default to zero, not recommended in GSEA
+#' @importFrom MKmisc mod.t.test
 #' @return GSEA results from clusterProfiler
 #' @export
 doGSEA <- function(stana, candSp=NULL, cl=NULL, eps=1e-2, how=mean,
@@ -47,6 +48,12 @@ doGSEA <- function(stana, candSp=NULL, cl=NULL, eps=1e-2, how=mean,
     if (target!="pathway") {
 	    url <- "https://rest.kegg.jp/link/ko/module"	
     }
+
+    bfc <- BiocFileCache()
+    path <- bfcrpath(bfc, url)
+
+    ## Load, transparent and rasterize
+    magick_image <- image_read(path)
 
     kopgsea <- data.frame(data.table::fread(url, header = FALSE, sep = "\t"))
     if (target=="pathway") {