diff w4mcorcov_calc.R @ 14:90708fdbc22d draft default tip

"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
author eschen42
date Wed, 18 Nov 2020 18:53:37 +0000
parents 2ae2d26e3270
children
line wrap: on
line diff
--- a/w4mcorcov_calc.R	Wed Dec 12 09:20:02 2018 -0500
+++ b/w4mcorcov_calc.R	Wed Nov 18 18:53:37 2020 +0000
@@ -22,8 +22,8 @@
       , algoC  = x_algorithm
       , predI  = 1
       , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0
-      , printL = FALSE
-      , plotL  = FALSE
+      , fig.pdfC = 'none'
+      , info.txtC  = 'none'
       , crossvalI = x_crossval_i
       , scaleC = "pareto" # data centered and pareto scaled here only. This line fixes issue #2.
       )
@@ -443,6 +443,7 @@
   # matchingC is one of { "none", "wildcard", "regex" }
   matchingC <- calc_env$matchingC
   labelFeatures <- calc_env$labelFeatures
+  minCrossvalI <- as.integer(calc_env$min_crossval_i)
 
   # arg/env checking
   if (!(facC %in% names(smpl_metadata))) {
@@ -600,7 +601,7 @@
                           }
         , x_show_labels = labelFeatures
         , x_progress    = progress_action
-        , x_crossval_i  = min(7, length(chosen_samples))
+        , x_crossval_i  = min(minCrossvalI, length(chosen_samples))
         , x_env         = calc_env
         )
         if ( is.null(my_cor_cov) ) {
@@ -674,7 +675,7 @@
                               }
             , x_show_labels = labelFeatures
             , x_progress    = progress_action
-            , x_crossval_i  = min(7, length(chosen_samples))
+            , x_crossval_i  = min(minCrossvalI, length(chosen_samples))
             , x_env         = calc_env
             )
             if ( is.null(my_cor_cov) ) {
@@ -753,7 +754,7 @@
                 , x_prefix      = "Features"
                 , x_show_labels = labelFeatures
                 , x_progress    = progress_action
-                , x_crossval_i  = min(7, length(chosen_samples))
+                , x_crossval_i  = min(minCrossvalI, length(chosen_samples))
                 , x_env         = calc_env
                 )
                 if ( is.null(my_cor_cov) ) {
@@ -806,7 +807,7 @@
               , x_prefix      = "Features"
               , x_show_labels = labelFeatures
               , x_progress    = progress_action
-              , x_crossval_i  = min(7, length(chosen_samples))
+              , x_crossval_i  = min(minCrossvalI, length(chosen_samples))
               , x_env         = calc_env
               )
               if ( is.null(my_cor_cov) ) {