updates

pdimens · Mar 3, 2022 · 47fa7ae · 47fa7ae
1 parent c2048f3
commit 47fa7ae
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Showing 7 changed files with 47 additions and 49 deletions.
diff --git a/.misc/meta.yml b/.misc/meta.yml
@@ -1,4 +1,4 @@
-{% set version = "3.6.2" %}
+{% set version = "3.6.3" %}
 {% set sha256 = "0f0998ecd50b586d69b50e53d9a0b3d5aa3afa70bd96fe85c2fa3ba02e58278b" %}
 
 package:

diff --git a/scripts/LASummary.r b/scripts/LASummary.r
@@ -1,7 +1,7 @@
 #! /usr/bin/env Rscript
 
-library(dplyr)
-library(tidyr)
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(tidyr))
 library(ggplot2)
 library(readr)
 

diff --git a/scripts/LepWrapTrim.r b/scripts/LepWrapTrim.r
@@ -1,7 +1,7 @@
 #! /usr/bin/env Rscript
 
-library(dplyr)
-library(tidyr)
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(tidyr))
 library(ggplot2)
 
 args <- commandArgs(trailingOnly = TRUE)

diff --git a/scripts/MapSummary.r b/scripts/MapSummary.r
@@ -21,47 +21,46 @@ if (file_test("-f", args[1])) {
 
 # if args[1] is the target directory
 } else if (file_test("-d", args[1])) {
-library(stringr)
-targetdir <- args[1]
+  library(stringr)
+  targetdir <- args[1]
 
-# pattern match to find the map files
-flist <- list.files(targetdir, full.names = TRUE, pattern = "^LOD.")
-# natural language sort
-flist <- str_sort(flist, numeric = TRUE)
+  # pattern match to find the map files
+  flist <- list.files(targetdir, full.names = TRUE, pattern = "^LOD.")
+  # natural language sort
+  flist <- str_sort(flist, numeric = TRUE)
 
-for (i in flist){
-  # pull the file name from the end
-  mapfile <- tail(strsplit(i, "\\/")[[1]], n = 1)
-  # pull out the LOD value
-  lod<- strsplit(mapfile, "\\.")[[1]][2]
-  # read in the file
-  .dat <- read.table(i, header = FALSE, skip = 1)
-  # make a table of counts
-  .counts <- as.data.frame(table(.dat$V1))
-  # rename columns
-  names(.counts) <- c("LG", paste0("LOD.", lod))
-  if (i == flist[1]){
-    # if it's the first file, instantiate the counts dataframe
-    summtable <- .counts
-  } else {
-    # otherwise do a matchy-matchy (outer join) to update/bind the dataframe
-    summtable <- merge(summtable, .counts, by = "LG", all.x = TRUE, all.y = TRUE)
+  for (i in flist){
+    # pull the file name from the end
+    mapfile <- tail(strsplit(i, "\\/")[[1]], n = 1)
+    # pull out the LOD value
+    lod<- strsplit(mapfile, "\\.")[[1]][2]
+    # read in the file
+    .dat <- read.table(i, header = FALSE, skip = 1)
+    # make a table of counts
+    .counts <- as.data.frame(table(.dat$V1))
+    # rename columns
+    names(.counts) <- c("LG", paste0("LOD.", lod))
+    if (i == flist[1]){
+      # if it's the first file, instantiate the counts dataframe
+      summtable <- .counts
+    } else {
+      # otherwise do a matchy-matchy (outer join) to update/bind the dataframe
+      summtable <- merge(summtable, .counts, by = "LG", all.x = TRUE, all.y = TRUE)
+    }
   }
-}
-
-# replace NA's as 0
-summtable[is.na(summtable)] <- 0
-summtable <- summtable[order(summtable$LG),]
 
-# generate output filenames
-out_tmp <-paste0(targetdir, "/.all.LOD.summary")
-out_file <- paste0(targetdir, "/all.LOD.summary")
+  # replace NA's as 0
+  summtable[is.na(summtable)] <- 0
+  summtable <- summtable[order(summtable$LG),]
 
-write.table(summtable, file = out_tmp, quote = FALSE, row.names = FALSE, col.names = TRUE)
-# use GNU column command to make the table fixed-width and remove the tmp file
-cmd <- paste("column -t", out_tmp, ">", out_file, "&& rm", out_tmp)
-system(cmd)
+  # generate output filenames
+  out_tmp <-paste0(targetdir, "/.all.LOD.summary")
+  out_file <- paste0(targetdir, "/all.LOD.summary")
 
+  write.table(summtable, file = out_tmp, quote = FALSE, row.names = FALSE, col.names = TRUE)
+  # use GNU column command to make the table fixed-width and remove the tmp file
+  cmd <- paste("column -t", out_tmp, ">", out_file, "&& rm", out_tmp)
+  system(cmd)
 } else {
   cat("Error: the argument must be either a mapfile or a directory of mapfiles")
 }
diff --git a/scripts/MarkerPlot.r b/scripts/MarkerPlot.r
@@ -1,7 +1,7 @@
 #! /usr/bin/env Rscript
 
-library(dplyr)
-library(tidyr)
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(tidyr))
 library(ggplot2)
 
 args <- commandArgs(trailingOnly = TRUE)

diff --git a/scripts/RecombinationSummary.r b/scripts/RecombinationSummary.r
@@ -1,10 +1,10 @@
 #! /usr/bin/env Rscript
 
 # This script will parse all the recombination logs of LepWrap
-library(dplyr)
-library(tidyr)
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(tidyr))
 library(stringr)
-library(purrr)
+suppressPackageStartupMessages(library(purrr))
 
 ## setup outfile
 # format trailing arguments for script

diff --git a/scripts/TrimSummaryPlot.r b/scripts/TrimSummaryPlot.r
@@ -1,7 +1,7 @@
 #! /usr/bin/env Rscript
 
-suppressMessages(library(dplyr))
-suppressPackageStartupMessages((library(tidyr))
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(tidyr))
 library(ggplot2)
 library(readr)
 
@@ -28,5 +28,4 @@ tbl %>%
        ) +
     scale_y_continuous(limits =   c(-0.05, max(tbl$n_removed)+10))
 
-ggsave(paste0(args[1], ".pdf"), height = 4, width = 7, units = "in")
-#ggsave(paste0(args[1], ".svg"), height = 4, width = 7, units = "in")
+ggsave(paste0(args[1], ".pdf"), height = 4, width = 7, units = "in")