order process by category and pipeline order

benchmark/plots.r

@@ -3,6 +3,7 @@ install.packages("ggplot2")
 library(tidyverse)
 library(ggplot2)
 library(dplyr)
+library(forcats)
 
 df <- read.csv("/home/mcroiset/HiC/benchmark/recap.txt", sep = "\t", header = TRUE)
 
@@ -79,7 +80,50 @@ df$file <- filenames
 
 important_processes <- c(15, 16, 17, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1,1,1,1,1,9,1,2,5,6,1,1,1,1,1,15,11,1,1,1,1,12,1,1,1,1,1)
 
-pdf("process_time.pdf")
+categories <- character(0)
+for (x in df$name) {
+  if (grepl('\\w*_ALIGN\\w*', x) || grepl('\\w*TRIM\\w*', x) || grepl('MERGE_BOWTIE2', x)) {
+    categories <- append(categories, "align")
+  }
+  else if (grepl('\\w*COOLER\\w*', x)) {
+    categories <- append(categories, "cooler")
+  }
+  else if (grepl('\\w*PAIRS\\w*', x)) {
+    categories<- append(categories, "pairs")
+  }
+  else if (grepl('\\w*MATRIX\\w*', x)) {
+    categories<- append(categories, "matrix")
+  }
+  else if (grepl('\\w*FILTER\\w*', x) || grepl('\\w*PICARD\\w*', x) || grepl('\\w*SAMTOOLS\\w*', x)) {
+    categories<- append(categories, "filter")
+  }
+  else if (grepl('\\w*CUTSITE\\w*', x)) {
+    categories<- append(categories, "cutsite")
+  }
+  else if (grepl('\\w*ITERALIGN\\w*', x)) {
+    categories<- append(categories, "iteralign")
+  }
+  else if (grepl('\\w*SAMPLESHEET\\w*', x) || (grepl('BOWTIE2_BUILD', x) || grepl('\\w*GETCHROM\\w*', x) || grepl('\\w*GET_RESTRIC\\w*', x))) {
+    categories<- append(categories, "data_prep")
+  }
+  else {
+    categories <- append(categories, "n")
+  }
+}
+# categories
+df$categorie <- categories
+
+print(levels(as.factor(df$name)))
+ordered_processes <- tibble(levels(as.factor(df$name)))
+order <- c(18, 7, 8, 7, 2, 20, 21, 14, 24, 23, 27, 22, 25, 30, 31, 32, 3, 6, 5, 19, 13, 19, 9, 4, 15, 28, 29, 18, 7, 8, 17, 16, 33, 11, 1, 10, 12, 27, 8)
+ordered_processes <- ordered_processes %>% add_column(order = order)
+ordered_processes <- rename(ordered_processes, name = `levels(as.factor(df$name))`)
+
+df <- left_join(df, ordered_processes, by= c("name" = "name"))
+
+
+
+# pdf("process_time.pdf")
 
 ggplot(df, aes(x = name, y = duration_minutes)) +
   geom_point(aes(color = name, shape = name)) +
@@ -91,15 +135,15 @@ ggplot(df, aes(x = name, y = duration_minutes)) +
   theme(axis.text.x=element_blank(), axis.ticks.x=element_blank()) + 
   ggtitle("Duration time of each process")
 
-ggplot(df, aes(x = name, y = realtime_minutes)) +
-  geom_point(aes(color = name, shape = name)) +
+ggplot(df, aes(x = fct_reorder(name, order), y = realtime_minutes)) +
+  geom_point(aes(color = categorie)) +
   scale_shape_manual(values = important_processes) +
   facet_wrap(~ file, ncol = 8) +
-  scale_y_continuous(breaks = seq(0, 490, by = 30)) +
   xlab("Processes") +
   ylab("Duration in minutes") +
   theme(axis.text.x=element_blank(), axis.ticks.x=element_blank())+ 
-  ggtitle("Real execution time of each process")
+  ggtitle("Real execution time of each process") +
+  scale_y_log10()
 
 
-dev.off()
+# dev.off()