diff sleuth.R @ 0:5f1cb4c28d73 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sleuth.R	Thu Jun 01 07:56:00 2023 +0000
@@ -0,0 +1,116 @@
+library(sleuth,
+        quietly = TRUE,
+        warn.conflicts = FALSE)
+library(annotables, quietly = TRUE, warn.conflicts = FALSE)
+library(argparse, quietly = TRUE, warn.conflicts = FALSE)
+library(tidyverse)
+
+
+# setup R error handling to go to stderr
+options(
+  show.error.messages = FALSE,
+  error = function() {
+    cat(geterrmessage(), file = stderr())
+    q("no", 1, FALSE)
+  }
+)
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+################################################################################
+### Input Processing
+################################################################################
+
+
+# Collect arguments from command line
+parser <- ArgumentParser(description = "Sleuth R script")
+
+parser$add_argument("--factorLevel", action = "append", required = TRUE)
+parser$add_argument("--factorLevel_counts",
+                    action = "append",
+                    required = TRUE)
+parser$add_argument("--factorLevel_n", action = "append",  required = TRUE)
+parser$add_argument("--cores",  type = "integer", required = TRUE)
+parser$add_argument("--normalize", action = "store_true", required = FALSE)
+parser$add_argument("--nbins", type = "integer", required = TRUE)
+parser$add_argument("--lwr", type = "numeric", required = TRUE)
+parser$add_argument("--upr", type = "numeric", required = TRUE)
+
+args <- parser$parse_args()
+
+all_files <- args$factorLevel_counts
+
+conditions <- c()
+for (x in seq_along(args$factorLevel)) {
+  temp <- append(conditions, rep(args$factorLevel[[x]]))
+  conditions <- temp
+}
+
+sample_names <- all_files %>%
+  str_replace(pattern = "\\.tab", "")
+
+design <-
+  data.frame(list(
+    sample = sample_names,
+    condition = conditions,
+    path = all_files
+  ))
+so <- sleuth_prep(design,
+                  cores = args$cores,
+                  normalize = args$normalize)
+
+so <- sleuth_fit(
+  so,
+  ~ condition,
+  "full",
+  n_bins = args$nbins,
+  lwr = args$lwr,
+  upr = args$upr
+)
+
+so <- sleuth_fit(
+  so,
+  ~ 1,
+  "reduced",
+  n_bins = args$nbins,
+  lwr = args$lwr,
+  upr = args$upr
+)
+
+so <- sleuth_lrt(so, "reduced", "full")
+
+sleuth_table <-
+  sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
+
+write.table(
+  sleuth_table,
+  file = "sleuth_table.tab",
+  quote = FALSE,
+  sep = "\t",
+  col.names = TRUE,
+  row.names = FALSE
+)
+
+
+outputFile <- file.path(getwd(), "pca_plot.pdf")
+pdf(file = outputFile,
+    height = 6,
+    width = 9)
+plot_pca(so, color_by = "condition")
+dev.off()
+
+outputFile <- file.path(getwd(), "group_density.pdf")
+pdf(file = outputFile,
+    height = 6,
+    width = 9)
+plot_group_density(
+  so,
+  use_filtered = TRUE,
+  units = "est_counts",
+  trans = "log",
+  grouping = setdiff(colnames(so$sample_to_covariates),
+                     "sample"),
+  offset = 1
+)
+dev.off()