Commit 9ce66a37 authored by Melanie Schneider's avatar Melanie Schneider

new names

parent 2b5d595c
......@@ -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()
......
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