new names

dge_workflow/cutadapt_summary.R

@@ -77,7 +77,7 @@ genTable1 <- function(logFile){
     No_of_processed_Reads=(paste("grep -F 'Processed reads' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9]+") %>% unlist() %>% as.numeric())[2],
     No_of_processed_Bases=(paste("grep -F 'Processed bases' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9]+") %>% unlist() %>% as.numeric())[2],
     Trimmed_Reads=(paste("grep -F 'Trimmed reads' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[3],
-    Quality-trimmed=(paste("grep -F 'Quality-trimmed' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[4],
+    Quality_trimmed=(paste("grep -F 'Quality-trimmed' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[4],
     Trimmed_Bases=(paste("grep -F 'Trimmed bases' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[4],
     Too_short_Reads=(paste("grep -F 'Too short reads' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[3]
   )
@@ -114,7 +114,7 @@ write.delim(adapterTrimmingStats, file="cutadapt_summary.adapterTrimmingStats.tx
 ggplot(trimmingStats, aes(Run, No_of_processed_Reads)) + geom_bar(stat='identity') + coord_flip()
 ggplot(trimmingStats, aes(Run, No_of_processed_Bases)) + geom_bar(stat='identity') + coord_flip()
 ggplot(trimmingStats, aes(Run, Trimmed_Reads)) + geom_bar(stat='identity') + coord_flip()
-ggplot(trimmingStats, aes(Run, Quality-trimmed)) + geom_bar(stat='identity') + coord_flip()
+ggplot(trimmingStats, aes(Run, Quality_trimmed)) + geom_bar(stat='identity') + coord_flip()
 ggplot(trimmingStats, aes(Run, Trimmed_Bases)) + geom_bar(stat='identity') + coord_flip()
 ggplot(trimmingStats, aes(Run, Too_short_Reads)) + geom_bar(stat='identity') + coord_flip()