updated

Author: software-github

MCA/analysis_library.R

@@ -210,14 +210,14 @@ calculate_cluster <- function(cluster_index,
 }
 
 # plot the bun values
-plot_bun_value <- function(bun_value,annotation_info){
+plot_dun_value <- function(dun_value,annotation_info){
 
   # Parameter in the function
-  # bun_value: the bun values
+  # dun_value: the bun values
   # annotation_info: the cell annotation information
 
   # calculate the log2 values
-  index_tmp = -log2(bun_value)
+  index_tmp = -log2(dun_value)
 
   # prepare the data for the boxplot
   longData = melt(as.matrix(index_tmp))
@@ -303,28 +303,28 @@ pdf_dun_tsne <- function(tissue_name){
 
   cluster_n = unique(knn5)
 
-  bun_value = c()
+  dun_value = c()
 
   for(i in c(1:dim(annotation_info)[1])){
 
     if(i %in% cluster_n){
 
       tmp_val = calculate_cluster(i,as.numeric(knn5),data_tsne)
 
-      bun_value = cbind(bun_value,tmp_val[[1]])
+      dun_value = cbind(dun_value,tmp_val[[1]])
 
     }else{
 
-      bun_value = cbind(bun_value,c(1,1,1,1,1,1))
+      dun_value = cbind(dun_value,c(1,1,1,1,1,1))
 
     }
 
   }
 
-  pp = plot_bun_value(bun_value,annotation_info)
+  pp = plot_dun_value(dun_value,annotation_info)
 
   ggsave(
-    filename = paste0(tissue_name, "_tsne_bun_index.pdf"),
+    filename = paste0(tissue_name, "_tsne_dun_index.pdf"),
     plot = pp,
     width = 8,
     height = 6
@@ -389,28 +389,28 @@ pdf_dun_tsne1 = function(tissue_name){
 
   cluster_n = unique(knn5)
 
-  bun_value = c()
+  dun_value = c()
 
   for(i in c(1:dim(annotation_info)[1])){
 
     if(i %in% cluster_n){
 
       tmp_val = calculate_cluster(i,as.numeric(knn5),data_tsne)
 
-      bun_value = cbind(bun_value,tmp_val[[1]])
+      dun_value = cbind(dun_value,tmp_val[[1]])
 
     }else{
 
-      bun_value = cbind(bun_value,c(1,1,1,1,1,1))
+      dun_value = cbind(dun_value,c(1,1,1,1,1,1))
 
     }
 
   }
 
-  pp = plot_bun_value(bun_value,annotation_info)
+  pp = plot_dun_value(dun_value,annotation_info)
 
   ggsave(
-    filename = paste0(tissue_name, "_tsne_bun_index.pdf"),
+    filename = paste0(tissue_name, "_tsne_dun_index.pdf"),
     plot = pp,
     width = 8,
     height = 6

MCA/analysis_main.R

@@ -834,13 +834,3 @@ for(i in c(1:6)){
 }
 
 # ---------------------------------------------------------------------------------
-
-
-
-
-
-
-
-
-
-

README.md

@@ -1,3 +1,5 @@
+[![DOI](https://zenodo.org/badge/173669168.svg)](https://zenodo.org/badge/latestdoi/173669168)
+
 # SCRABBLE_PAPER
 
 Data and analysis for the paper "Single-cell RNA-Seq imputation constrained by bulk RNA-Seq data".