Merge pull request #58 from ZhimingYe/ver0.8/StartUpFix

bump to 0.8.4

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: EnrichGT
 Title: EnrichGT - all in one enrichment analysis soluction
-Version: 0.8.2
+Version: 0.8.4
 Author: Zhiming Ye
 Maintainer: Zhiming Ye <[email protected]>
 Description: Do biological enrichment analysis and parsing and clustering

R/egt.R

@@ -65,7 +65,7 @@ setMethod("doEnrichGT", signature(x = "list"),function(x,...){
   clsObj<-.enrichpws(InnerDF$ID,InnerDF$geneID,ClusterNum,method)
   suppressMessages({InnerDF<-InnerDF |> dplyr::left_join(clsObj[[1]])}) # Merge according to "ID"
   if(sum(colnames(InnerDF)=="Up_Vs_Down")>0){
-    InnerDF<-InnerDF |> dplyr::filter(pvalue<0.05,Count>=5,p.adjust<P.adj) |> dplyr::mutate(geneID=paste0("/@Up_Genes@: /",UpGenes,"/@Down_Genes@: /",DownGenes)) |> dplyr::select(ID,Description,GeneRatio,`p.adjust`,geneID,Cluster,Count,Up_Vs_Down)
+    InnerDF<-InnerDF |> dplyr::filter(pvalue<0.05,Count>=5,p.adjust<P.adj) |> dplyr::mutate(geneID=paste0("@Up_Genes@: /",UpGenes,"/@Down_Genes@: /",DownGenes)) |> dplyr::select(ID,Description,GeneRatio,`p.adjust`,geneID,Cluster,Count,Up_Vs_Down)
   }else{
     InnerDF<-InnerDF |> dplyr::filter(pvalue<0.05,Count>=5,p.adjust<P.adj) |> dplyr::select(ID,Description,GeneRatio,`p.adjust`,geneID,Cluster,Count) # Need Fix
   }
@@ -105,6 +105,7 @@ remove_more_updownInfo <- function(x){
   x <- lapply(x,function(x){
     x <- x[!grepl("Up_Genes",x)]
     x <- x[!grepl("Down_Genes",x)]
+    x <- x[x!=""]
     return(x)
   })
 }

R/interface.R

@@ -44,7 +44,7 @@
 #' @export
 #'
 #' @author Zhiming Ye
-egt_recluster_analysis<-function(x,ClusterNum=17,P.adj=0.05,force=F,nTop=10,method="ward.D2",...){
+egt_recluster_analysis<-function(x,ClusterNum=10,P.adj=0.05,force=F,nTop=10,method="ward.D2",...){
   objname<-deparse(substitute(x))
   if(objname=="."){
     objname<-"`Magrittr` pipe conveyed object"

README.md

@@ -1,8 +1,8 @@
 # EnrichGT 0.8
 
-**EnrichGT \<-** Fast, light weight enrichment analysis + insightful re-clustering results make all results explainable + Pretty HTML tables, Just in **ONE** package, 
+**EnrichGT \<-** Fast, light weight enrichment analysis + insightful re-clustering results make all results explainable + Pretty HTML tables, Just in **ONE** package, designed for researchers in wet-labs. 
 
-Please see the package website: <https://zhimingye.github.io/EnrichGT/>
+Please see the package website for more info: <https://zhimingye.github.io/EnrichGT/>
 
 ![](https://zhimingye.github.io/EnrichGT/enrichGTTable.jpg)