fix plotGSEA volcano function and update readme

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: genekitr
 Type: Package
 Title: Gene Analysis Toolkit in R
-Version: 0.8.4
+Version: 0.8.5
 Authors@R: 
     c(person(given = "Yunze",
              family = "Liu",

R/genGO.R

@@ -38,8 +38,7 @@
 #'
 #' gego <- genGO(id, group_list = group,
 #'   org = "human", ont = "bp", pvalueCutoff = 0.1,
-#'   qvalueCutoff = 1
-#' )
+#'   qvalueCutoff = 1)
 #'
 #' }
 genGO <- function(id,

R/plotGSEA.R

@@ -83,11 +83,11 @@ plotGSEA <- function(gsea_list,
   if(plot_type == 'volcano'){
     gsea_df <- gsea_list$gsea_df
     gsea_df <- gsea_df[order(gsea_df$NES,decreasing = TRUE),]
+    plot_df <- gsea_df
     if(is.numeric(show_pathway)){
-      plot_df = gsea_df
       plot_df$group <- c(rep('high',show_pathway),rep('ignore',nrow(plot_df)-2*show_pathway),rep('low',show_pathway))
     }else{
-      nes <- plot_df[gsea_df$Description %in% show_pathway,'NES']
+      nes <- plot_df[plot_df$Description %in% show_pathway,'NES']
       plot_df$group <- 'ignore'
       plot_df[plot_df$Description %in% show_pathway,'group'] <- sapply(nes, function(x) ifelse(x>0,'high','low'))
     }

R/plotVenn.R

@@ -33,12 +33,10 @@
 #' )
 #' plotVenn(sm_gene_list,
 #'   text_size = 1.5, alpha_degree = 1,
-#'   remove_grid = TRUE, color = ggsci::pal_lancet()(3)
-#' )
+#'   remove_grid = TRUE, color = ggsci::pal_lancet()(3))
 #' plotVenn(la_gene_list,
 #'   text_size = 15, alpha_degree = 0.2, border_thick = 2,
-#'   remove_grid = TRUE, use_venn = FALSE
-#' )
+#'   remove_grid = TRUE, use_venn = FALSE)
 plotVenn <- function(venn_list,
                      use_venn = TRUE,
                      color = NULL,

README.md

@@ -1,6 +1,6 @@
 <img src="https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2022-05-24-043213.png" align="left" width="200"/>
 
-[![CRANstatus](https://www.r-pkg.org/badges/version/genekitr)](https://cran.r-project.org/package=genekitr) [![](https://img.shields.io/badge/devel%20version-0.8.4-green.svg)](https://github.com/GangLiLab/genekitr) [![](https://cranlogs.r-pkg.org/badges/grand-total/genekitr?color=orange)](https://cran.r-project.org/package=genekitr) [![lifecycle](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) 
+[![CRANstatus](https://www.r-pkg.org/badges/version/genekitr)](https://cran.r-project.org/package=genekitr) [![](https://img.shields.io/badge/devel%20version-0.8.5-green.svg)](https://github.com/GangLiLab/genekitr) [![](https://cranlogs.r-pkg.org/badges/grand-total/genekitr?color=orange)](https://cran.r-project.org/package=genekitr) [![lifecycle](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) 
 
 ![Alt](https://repobeats.axiom.co/api/embed/e42ba06d30de893670c70324f19398ef0a7c26fa.svg "Repobeats analytics image")
 
@@ -37,7 +37,9 @@ Here, I want to tell you a story about Mr. Doodle, a computational biology stude
 
 PI gave Doodle 30 genes and let him check their locations (better with sequences) and exact names. Doodle searched on NCBI one by one and copied & paste it into excel. Doodle sent the file to PI one hour later, and PI smiled, "Well done! Now I have another 50!" 
 
-<b style='color:#486CBE'>**Doodle wonders how to avoid this repeat searching work?**</b>
+```diff
+! Doodle wonders how to avoid this repeat searching work? (and bold)
+```
 
 ### Scene 2: embarrassing name