diff w4mclassfilter_wrapper.R @ 14:87ec0d3c2266 draft

"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"

--- a/w4mclassfilter_wrapper.R	Thu Oct 24 10:21:23 2019 -0400
+++ b/w4mclassfilter_wrapper.R	Fri Jan 03 11:07:39 2020 -0500
@@ -23,8 +23,16 @@
 
 suppressMessages(library(w4mclassfilter))
 
-if(packageVersion("w4mclassfilter") < "0.98.12")
-    stop("Please use 'w4mclassfilter' versions of 0.98.12 and above")
+expected_version <- "0.98.18"
+actual_version <- packageVersion("w4mclassfilter")
+if(packageVersion("w4mclassfilter") < expected_version) {
+    stop(
+         sprintf(
+             "Unrecoverable error: Version %s of the 'w4mclassfilter' R package was loaded instead of expected version %s",
+             actual_version, expected_version
+         )
+    )
+}
 
 ## constants
 ##----------
@@ -104,8 +112,14 @@
 classnameColumn <- as.character(argVc["classnameColumn"])
 samplenameColumn <- as.character(argVc["samplenameColumn"])
 
-order_smpl <- as.character(argVc["order_smpl"])
 order_vrbl <- as.character(argVc["order_vrbl"])
+centering <- as.character(argVc["centering"])
+order_smpl <-
+  if (centering == 'centroid' || centering == 'median') {
+    "sampleMetadata"
+  } else {
+    as.character(argVc["order_smpl"])
+  }
 
 variable_range_filter <- as.character(argVc["variable_range_filter"])
 variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]]
@@ -115,6 +129,8 @@
 ## -----------------------------
 my_transformation_and_imputation <- if (transformation == "log10") {
   function(m) {
+    # convert negative intensities to missing values
+    m[m < 0] <- NA
     if (!is.matrix(m))
       stop("Cannot transform and impute data - the supplied data is not in matrix form")
     if (nrow(m) == 0)
@@ -130,6 +146,8 @@
   }
 } else if (transformation == "log2") {
   function(m) {
+    # convert negative intensities to missing values
+    m[m < 0] <- NA
     if (!is.matrix(m))
       stop("Cannot transform and impute data - the supplied data is not in matrix form")
     if (nrow(m) == 0)
@@ -144,8 +162,21 @@
     return ( my_imputation_function(m) )
   }
 } else {
-  # use the method from the w4mclassfilter class
-  my_imputation_function
+  function(m) {
+    # convert negative intensities to missing values
+    m[m < 0] <- NA
+    if (!is.matrix(m))
+      stop("Cannot transform and impute data - the supplied data is not in matrix form")
+    if (nrow(m) == 0)
+      stop("Cannot transform and impute data - data matrix has no rows")
+    if (ncol(m) == 0)
+      stop("Cannot transform and impute data - data matrix has no columns")
+    suppressWarnings({
+      # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
+      m[is.na(m)] <- NA
+    })
+    return ( my_imputation_function(m) )
+  }
 }
 
 ##------------------------------
@@ -165,6 +196,7 @@
 , samplename_column     = samplenameColumn
 , order_vrbl            = order_vrbl
 , order_smpl            = order_smpl
+, centering             = centering
 , variable_range_filter = variable_range_filter
 , failure_action        = my_print
 , data_imputation       = my_transformation_and_imputation