Merge pull request #55 from ZhimingYe/ver0.8/StartUpFix

Version 0.7.5 minimal fix for actual usage

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: EnrichGT
 Title: EnrichGT - all in one enrichment analysis soluction
-Version: 0.7.0
+Version: 0.7.4
 Author: Zhiming Ye
 Maintainer: Zhiming Ye <[email protected]>
 Description: Do biological enrichment analysis and parsing and clustering

R/figures.R

@@ -3,7 +3,8 @@
 #' @description
 #' This plot is the most widely like `enrichplot::dotplot()`used method to visualize enriched terms. It shows the enrichment scores (e.g. p values) and gene ratio or NES as dot size and color / or bar height. Users can specify the number of terms using `ntop` or selected terms to color via the `low.col` and `hi.col`.
 #' @param x a data frame form enriched result like `egt_enrichment_analysis()` or `egt_gsea_analysis()`, or an re-clustered `EnrichGT` object
-#' @param ntop Show top N in each cluster
+#' @param ntop Show top N in each cluster. In default, for origin enriched result, showing top 15; for re-clustered object, showing top 5 in each cluster. 
+#' @param showIDs bool, show pathway IDs or not. Default is FALSE
 #' @param low.col the color for the lowest
 #' @param hi.col the color for the highest
 #' @param max_len_descript the label format length, default as 40.
@@ -35,12 +36,21 @@
 #' @importFrom methods is
 #' @importFrom forcats fct_reorder
 #' @author Zhiming Ye
-egt_plot_results <- function(x,ntop=30,...,P.adj=NULL){
+egt_plot_results <- function(x,ntop=NULL,showIDs=F,max_len_descript=40,...,P.adj=NULL){
+  if(is.null(ntop)){
+    ntop <- 15
+  }
   if(class(x)[1]=="EnrichGT_obj"){
+    if(is.null(ntop)){
+        ntop <- 5
+    }
+    if(x@fused){
+      cli::cli_alert_info("Found a fused EnrichGT_obj, you can set showIDs=T to show the source database the pathways from. ")
+    }
     if(sum(colnames(x@enriched_result)=="absNES")==0){
-      figure0<-ORA2dp(x,...)
+      figure0<-ORA2dp(x,ntop=ntop,showIDs=showIDs,max_len_descript=max_len_descript,...)
     }else{
-      figure0<-GSEA2dp(x,...)
+      figure0<-GSEA2dp(x,ntop=ntop,showIDs=showIDs,max_len_descript=max_len_descript,...)
     }
   }else if(is.data.frame(x)){
     plotingTemp <- new.env()
@@ -70,7 +80,7 @@ egt_plot_results <- function(x,ntop=30,...,P.adj=NULL){
         dplyr::arrange(desc(absNES), .by_group = TRUE) |>
         dplyr::slice_head(n = round(round(ntop / 2) + 1 + round(ntop/20))) |> # For balance
         dplyr::ungroup() # Balance up and down
-      figure0<-GSEA2dp(obj,ntop=ntop,...)
+      figure0<-GSEA2dp(obj,ntop=ntop,showIDs=showIDs,max_len_descript=max_len_descript,...)
     }else{
       InnerDF<-x |> dplyr::filter(p.adjust<(plotingTemp$PadjVal)) |> dplyr::select(ID,Description,GeneRatio,`p.adjust`,geneID,Count) # Need Fix
       obj<-InnerDF |>
@@ -84,7 +94,7 @@ egt_plot_results <- function(x,ntop=30,...,P.adj=NULL){
         dplyr::arrange(desc(Count), .by_group = TRUE) |>
         dplyr::slice_head(n = 2) |>
         dplyr::ungroup()
-      figure0<-ORA2dp(obj,ntop=ntop,...)
+      figure0<-ORA2dp(obj,ntop=ntop,showIDs=showIDs,max_len_descript=max_len_descript,...)
     }
   }
   return(figure0)
@@ -119,7 +129,7 @@ egt_plot_umap <- function(x,...){
   return(px)
 }
 
-ORA2dp<-function(x,ntop = 7,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript=40,...){
+ORA2dp<-function(x,ntop = 7,showIDs=F,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript=40,...){
   if(is.list(x) & !is.data.frame(x)){
     cli::cli_abort("For a list object, please run plotting for every object inside list, instead of the whole list.")
   }
@@ -134,6 +144,11 @@ ORA2dp<-function(x,ntop = 7,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript=
     assign("df0",x,envir = TempPlotingEnv)
     cli::cli_alert_warning("You are drawing origin results, for better result you can re-cluster it by egt_recluster_analysis()")
   })
+  if(showIDs & (sum(TempPlotingEnv$df0$ID == TempPlotingEnv$df0$Description)>=5)){
+    TempPlotingEnv$df0$ID <- substr(TempPlotingEnv$df0$ID,1,15)
+    TempPlotingEnv$df0$Description <- paste0(TempPlotingEnv$df0$ID,":",TempPlotingEnv$df0$Description)
+    max_len_descript <- max_len_descript + 16
+  }
   tryCatch({
     df <- TempPlotingEnv$df0 |>
       group_by(Cluster) |>
@@ -148,7 +163,7 @@ ORA2dp<-function(x,ntop = 7,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript=
   return(px)
 }
 
-GSEA2dp<-function(x,ntop = 7,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript=40,...){
+GSEA2dp<-function(x,ntop = 7,showIDs=F,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript=40,...){
   if(is.list(x) & !is.data.frame(x)){
     cli::cli_abort("For a list object, please run plotting for every object inside list, instead of the whole list.")
   }
@@ -163,6 +178,11 @@ GSEA2dp<-function(x,ntop = 7,low.col="#ff6f81",hi.col="#78cfe5",max_len_descript
     assign("df0",x,envir = TempPlotingEnv)
     cli::cli_alert_warning("You are drawing origin results, for better result you can re-cluster it by egt_recluster_analysis()")
   })
+  if(showIDs & (sum(TempPlotingEnv$df0$ID == TempPlotingEnv$df0$Description)>=5)){
+    TempPlotingEnv$df0$ID <- substr(TempPlotingEnv$df0$ID,1,15)
+    TempPlotingEnv$df0$Description <- paste0(TempPlotingEnv$df0$ID,":",TempPlotingEnv$df0$Description)
+    max_len_descript <- max_len_descript + 16
+  }
   tryCatch({
     df <- TempPlotingEnv$df0 |>
       group_by(Cluster) |>

R/fuser.R

@@ -120,5 +120,6 @@ universalGT<-function(x,...){
   else{
     x1<-.genGT(x,...)
   }
+  x1@fused <- T
   return(x1)
 }

R/gt_generator.R

@@ -4,6 +4,9 @@ gt_gsea<-function(x,ClusterNum,objname,objname2=NULL,...){
   }
   orderlist<-fix_order(x$Cluster)
   orderlist<-orderlist[orderlist%in%x$Cluster]
+  if(sum(x$ID == x$Description)>=5){
+    x$ID <- paste0(objname," / ",1:nrow(x))
+  }
   y<-x |> gt::gt(groupname_col = "Cluster") |>
     gt_hulk_col_numeric2(Padj,pal = RColorBrewer::brewer.pal(8,"Spectral")) |>
     gt_hulk_col_numeric2(absNES,pal = RColorBrewer::brewer.pal(8,"PuBuGn") |> rev()) |>
@@ -33,6 +36,9 @@ gt_ora<-function(x,ClusterNum,objname,objname2=NULL,...){
   }
   orderlist<-fix_order(x$Cluster)
   orderlist<-orderlist[orderlist%in%x$Cluster]
+  if(sum(x$ID == x$Description)>=5){
+    x$ID <- paste0(objname," / ",1:nrow(x))
+  }
   y<-x |> gt::gt(groupname_col = "Cluster") |>
     gt_hulk_col_numeric2(PCT,pal = RColorBrewer::brewer.pal(8,"PiYG") |> rev()) |>
     gt_hulk_col_numeric2(Padj,pal = RColorBrewer::brewer.pal(8,"Spectral")) |>

R/interface.R

@@ -57,7 +57,7 @@ egt_recluster_analysis<-function(x,ClusterNum=17,P.adj=0.05,force=F,nTop=10,meth
   required_packages <- c(
     "dplyr", "fontawesome", "glue", "gt", "proxy",
     "RColorBrewer", "rlang", "scales", "text2vec",
-    "tibble","forcats","ggplot2","Matrix"
+    "tibble","forcats","ggplot2", "Matrix", "xfun"
   )
   missing_packages <- required_packages[!(required_packages %in% installed.packages()[,"Package"])]
 
@@ -73,7 +73,7 @@ egt_recluster_analysis<-function(x,ClusterNum=17,P.adj=0.05,force=F,nTop=10,meth
     require("Matrix")
     require("cli")
     cli::cli_h1("EnrichGT")
-    cli::cli_alert_info("View your enrichment result by entring `EnrichGT(result)`")
-    cli::cli_alert("by Zhiming Ye, https://github.com/ZhimingYe/EnrichGT")
+    cli::cli_alert_info("See help on https://zhimingye.github.io/EnrichGT/")
+    cli::cli_alert("by Zhiming Ye")
   }
 }

R/objFrame.R

@@ -4,7 +4,8 @@ setClass("EnrichGT_obj",slots=list(enriched_result="data.frame",
                                          pathway_clusters="list",
                                          document_term_matrix="dgCMatrix",
                                          clustering_tree="hclust",
-                                         raw_enriched_result="data.frame"))
+                                         raw_enriched_result="data.frame",
+                                         fused="logical"))
 
 
 setMethod("show", "EnrichGT_obj", function(object) {
@@ -23,6 +24,7 @@ new.egt <- function(x1,x2,x3,x4,x5,x6,x7){
     objegt@document_term_matrix <- x5
     objegt@clustering_tree <- x6
     objegt@raw_enriched_result <- x7
+    objegt@fused <- F
     flag0<-T
   },error=function(e){
     message_egt("Failed to create EnrichGT object! Please re-check your input.")