changeset 80:6d97ef6bf7b7 draft

Uploaded

--- a/ideas_genome_tracks.R	Wed Jan 03 14:36:01 2018 -0500
+++ b/ideas_genome_tracks.R	Thu Jan 04 12:31:30 2018 -0500
@@ -103,41 +103,44 @@
 create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_para, input_dir_state, build, chrom_len_file,
         tracks_dir, hub_name, hub_short_label, hub_long_label, state_indexes, state_names, 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);
-    ######
-    if (!is.null(state_indexes)) {
+    s_indexes = c();
+    s_names = c();
+    s_colors = c();
+    if (is.null(state_indexes)) {
+        # Generate state colors automatically.
+        index = 0;
+        para_files = list.files(path=input_dir_para, full.names=TRUE);
+        for (para_file in para_files) {
+            data_frame = read.table(para_file, comment="!", header=T);
+            color_hex_code = create_heatmap(data_frame);
+            s_indexes = c(s_indexes, index);
+            s_names = c(s_names, toString(index));
+            s_colors = c(s_colors, color_hex_code);
+        }
+    } else {
         # Split state_indexes into a list of integers.
-        s_indexes <- c();
-        index_str <- as.character(state_indexes);
-        items <- strsplit(index_str, ",")
+        index_str = as.character(state_indexes);
+        items = strsplit(index_str, ",")
         for (item in items) {
-            s_indexes <- c(s_indexes, as.integer(item));
+            s_indexes = c(s_indexes, as.integer(item));
         }
         # Split state_names into a list of strings.
-        s_names <- c();
-        name_str <- as.character(state_colors);
-        items <- strsplit(name_str, ",");
-        item_index <- 0;
+        name_str = as.character(state_colors);
+        items = strsplit(name_str, ",");
+        item_index = 0;
         for (item in items) {
             item_index = item_index + 1;
             # Handle the special string "use state index".
             if (identical(item, "use state index")) {
-                item <- s_indexes[item_index];
+                item = s_indexes[item_index];
             }
-            s_names <- c(s_names, item);
+            s_names = c(s_names, item);
         }
         # Split state_colors into a list of strings.
-        s_colors <- c();
-        color_str <- as.character(state_colors);
-        items <- strsplit(color_str, ",");
+        color_str = as.character(state_colors);
+        items = strsplit(color_str, ",");
         for (item in items) {
-            s_colors <- c(s_colors, item);
+            s_colors = c(s_colors, item);
         }
     }
     base_track_file_name <- paste(tracks_dir, hub_name, sep="");
@@ -145,16 +148,7 @@
     track_db = NULL;
     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);
-        } else {
-            # Use the selected color for the current state.
-            color_hex_code <- s_colors[i];
-        }
-        color <- paste(c(col2rgb(color_hex_code)), collapse=",");
+        color <- paste(c(col2rgb(s_colors[i])), collapse=",");
         # Get the bigDataUrl.
         big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build);
         # trackDb.txt track hub entry.