changeset 74:1c8322d11836 draft

Uploaded

--- a/ideas_genome_tracks.R	Thu Dec 21 11:17:03 2017 -0500
+++ b/ideas_genome_tracks.R	Tue Jan 02 10:21:13 2018 -0500
@@ -103,13 +103,6 @@
         chrom_len_file, tracks_dir, hub_name, short_label, long_label, state_indexes, state_colors) {
     # Create a trackDb.txt file that includes each state.
     para_files <- list.files(path=input_dir_para, full.names=TRUE);
-    ######
-    # The following is temporary and will be eliminated when there
-    # are multiple .para files.  See the comments in the for loop
-    # below.
-    data_frame <- read.table(para_files[1], comment="!", header=T);
-	color_hex_code <- create_heatmap(data_frame);
-    ######
     base_track_file_name <- paste(tracks_dir, hub_name, sep="");
     cells = create_track(input_dir_state, chrom_len_file, base_track_file_name);
     if (!is.null(state_indexes)) {
@@ -132,10 +125,8 @@
     for (i in 1:length(cells)) {
         # Get the color for the current state.
         if (is.null(state_indexes) || !is.element(i, s_indexes)) {
-            ######
-            # This is for future use since there is currently only a single .para file.
-            # data_frame <- read.table(para_files[i], comment="!", header=T);
-            # color_hex_code <- create_heatmap(data_frame);
+            data_frame <- read.table(para_files[i], comment="!", header=T);
+            color_hex_code <- create_heatmap(data_frame);
         } else {
             # Use the selected color for the current state.
             color_hex_code <- s_colors[i];
@@ -203,4 +194,3 @@
 
 # Create the primary HTML dataset.
 create_primary_html(opt$output_trackhub, tracks_dir, opt$build);
-