changeset 87:60ce288eb52f draft

Uploaded

--- a/ideas_genome_tracks.R	Fri Jan 05 13:54:44 2018 -0500
+++ b/ideas_genome_tracks.R	Fri Jan 05 13:56:36 2018 -0500
@@ -4,22 +4,22 @@
 suppressPackageStartupMessages(library("optparse"))
 
 option_list <- list(
-            make_option(c("--build"), action="store", dest="build", help="Genome build"),
-            make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", help="Chromosome length file"),
-            make_option(c("--email"),  action="store", dest="email", help="User email address"),
-            make_option(c("--galaxy_url"),  action="store", dest="galaxy_url", help="Galaxy instance base URL"),
-            make_option(c("--hub_long_label"), action="store", dest="hub_long_label", help="Hub long label"),
-            make_option(c("--hub_name"),  action="store", dest="hub_name", default=NULL, help="Hub name without spaces"),
-            make_option(c("--hub_short_label"), action="store", dest="hub_short_label", help="Hub short label"),
-            make_option(c("--input_dir_para"), action="store", dest="input_dir_para", help="Directory containing .para outputs from IDEAS"),
-            make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
-            make_option(c("--output_trackhub"),  action="store", dest="output_trackhub", help="Output hub file"),
-            make_option(c("--output_trackhub_files_path"),  action="store", dest="output_trackhub_files_path", help="Output hub extra files path"),
-            make_option(c("--output_trackhub_id"),  action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"),
-            make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
-            make_option(c("--state_colors"), action="store", dest="state_colors", default=NULL, help="List of state colors"),
-            make_option(c("--state_indexes"), action="store", dest="state_indexes", default=NULL, help="List of state indexes"),
-            make_option(c("--state_names"), action="store", dest="state_names", default=NULL, help="List of state names")
+        make_option(c("--build"), action="store", dest="build", help="Genome build"),
+        make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", help="Chromosome length file"),
+        make_option(c("--email"),  action="store", dest="email", help="User email address"),
+        make_option(c("--galaxy_url"),  action="store", dest="galaxy_url", help="Galaxy instance base URL"),
+        make_option(c("--hub_long_label"), action="store", dest="hub_long_label", help="Hub long label"),
+        make_option(c("--hub_name"),  action="store", dest="hub_name", default=NULL, help="Hub name without spaces"),
+        make_option(c("--hub_short_label"), action="store", dest="hub_short_label", help="Hub short label"),
+        make_option(c("--input_dir_para"), action="store", dest="input_dir_para", help="Directory containing .para outputs from IDEAS"),
+        make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
+        make_option(c("--output_trackhub"),  action="store", dest="output_trackhub", help="Output hub file"),
+        make_option(c("--output_trackhub_files_path"),  action="store", dest="output_trackhub_files_path", help="Output hub extra files path"),
+        make_option(c("--output_trackhub_id"),  action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"),
+        make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
+        make_option(c("--state_colors"), action="store", dest="state_colors", default=NULL, help="List of state colors"),
+        make_option(c("--state_indexes"), action="store", dest="state_indexes", default=NULL, help="List of state indexes"),
+        make_option(c("--state_names"), action="store", dest="state_names", default=NULL, help="List of state names")
 )
 
 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
@@ -88,6 +88,7 @@
         t0 = c(0, t) + 1;
         t = c(t, L);
         np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
+        #cat("JJJJJJJ as.numeric(np[,4]: ", as.numeric(np[,4]), "\n");
         track_file_name_bed_unsorted <- get_track_file_name(base_track_file_name, i, "bed_unsorted");
         track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
         track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
@@ -103,52 +104,84 @@
     return(cells);
 }
 
-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_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, specified_state_indexes, specified_state_names, specified_state_colors) {
     # Create a trackDb.txt file that includes each state.
-    s_indexes = c();
-    s_names = c();
-    s_colors = c();
-    # Generate the default state colors.
+    #cat("\n\n\n\n\nXXXXXXXXXXXXXXXX Entered create_track_db\n");
+    #cat("specified_state_indexes: ", specified_state_indexes, "\n");
+    #cat("specified_state_names: ", specified_state_names, "\n");
+    #cat("specified_state_colors: ", specified_state_colors, "\n");
+    state_names = c();
+    state_colors = list();
+    # Generate the default state names and colors.
+    # IDEAS state indexes are zero based.
     index = 0;
     para_files = list.files(path=input_dir_para, full.names=TRUE);
+    #cat("para_files: ", toString(para_files), "\n\n\n");
     for (para_file in para_files) {
+        #cat("para_file: ", para_file, "\n");
+        # Append the default state name.
+        state_names = c(state_names, toString(index));
+        #cat("\n", index,index,index,index, "state_names: ", state_names, "\n");
+        # Append the default color codes vector.
         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);
+        # Here specified_state_colors will look something like this:
+        # 248,239,0 254,153,95 255,255,255 245,245,0 #F8EF00 #FE995F #FFFFFF #F5F500
+        state_color_codes_vector = create_heatmap(data_frame);
+        #cat("state_color_codes_vector: ", state_color_codes_vector, "\n");
+        #cat("typeof(state_color_codes_vector): ", typeof(state_color_codes_vector), "\n");
+        #cat("length(state_color_codes_vector): ", length(state_color_codes_vector), "\n");
+        state_colors[[index + 1]] = state_color_codes_vector;
+        #cat("\n", index,index,index,index, "state_colors: ", state_colors, "\n");
         index = index + 1;
     }
-    if (!is.null(state_indexes)) {
+    #cat("\n\nBBBBBBBB default state_names: ", state_names, "\n");
+    #cat("BBBBBBBB default typeof(state_names): ", typeof(state_names), "\n");
+    #cat("BBBBBBBB default length(state_names): ", length(state_names), "\n");
+    #cat("BBBBBBBB default state_colors: ", toString(state_colors), "\n");
+    #cat("BBBBBBBB default length(state_colors): ", length(state_colors), "\n\n\n");
+    if (!is.null(specified_state_indexes)) {
         # Replace default name with specified name and default
         # color with specified color for each selected state.
-        # Split state_indexes into a list of strings.
-        index_str = as.character(state_indexes);
-        state_index_items = strsplit(index_str, ",");
-        # Split state_names into a list of strings.
-        name_str = as.character(state_names);
-        state_name_items = strsplit(name_str, ",");
-        # Split state_colors into a list of strings.
-        color_str = as.character(state_colors);
-        state_color_items = strsplit(color_str, ",");
+        # Split specified_state_indexes into a list of strings.
+        index_str = as.character(specified_state_indexes);
+        specified_state_index_items = strsplit(index_str, ",")[[1]];
+        # Split specified_state_names into a list of strings.
+        name_str = as.character(specified_state_names);
+        specified_state_name_items = strsplit(name_str, ",")[[1]];
+        # Split specified_state_colors into a list of strings.
+        color_str = as.character(specified_state_colors);
+        specified_state_color_items = strsplit(color_str, ",")[[1]];
         # Replace default names and colors.
-        specified_item_index = 1;
-        for (state_index_item in state_index_items) {
-            specified_index = as.integer(state_index_item);
+        loop_index = 1;
+        for (specified_state_index_item in specified_state_index_items) {
+            #cat("specified_state_index_item: ", specified_state_index_item, "\n");
+            specified_index = as.integer(specified_state_index_item);
+            #cat("specified_index: ", specified_index, "\n");
             # Replace default name with specified name.
-            specified_name = state_name_items[specified_item_index];
+            specified_name = specified_state_name_items[loop_index];
             # Handle the special string "use state index".
             if (identical(specified_name, "use state index")) {
-                specified_name = state_index_item;
+                specified_name = specified_state_index_item;
             }
-            s_names[specified_index] = specified_name;
+            #cat("specified_name: ", specified_name, "\n");
+            #cat("state_names: ", state_names, "\n");
+            #state_names[specified_index] = specified_name;
+            state_names = replace(state_names, state_names==specified_index, specified_name);
+            #cat("state_names: ", state_names, "\n");
             # Replace default color with specified color.
-            s_colors[specified_index] = state_color_items[specified_item_index];
+            #cat("specified_state_color_items[specified_item_index]: ", specified_state_color_items[specified_item_index], "\n");
+            # FixMe: replacing default state colors is not yet working.
+            #state_colors[specified_index] = specified_state_color_items[loop_index];
+            #cat("state_colors: ", toString(state_colors), "\n");
+            loop_index = loop_index + 1;
         }
     }
+    #cat("\n\nCCCCCC reset state_names: ", state_names, "\n");
+    #cat("CCCCCC reset state_colors: ", toString(state_colors), "\n");
+    #cat("CCCCCC reset length(state_colors): ", length(state_colors), "\n\n\n");
     base_track_file_name <- paste(tracks_dir, hub_name, sep="");
-    cells = create_cells(input_dir_state, chrom_len_file, base_track_file_name, s_indexes, s_names, s_colors);
+    cells = create_cells(input_dir_state, chrom_len_file, base_track_file_name, state_indexes, state_names, state_colors);
     cell_info = cbind(cells, cells, cells, "#000000");
     cell_info = array(cell_info, dim=c(length(cells), 4));
     cell_info = as.matrix(cell_info);
@@ -160,7 +193,27 @@
         }
         ii = ii[1];
         # Get the color for the current state.
-        color <- paste(c(col2rgb(s_colors[i])), collapse=",");
+        color_vector = state_colors[i];
+        #cat("color_vector: ", toString(color_vector), "\n");
+        # We are handling hte hub label color setting here.
+        # FixMe: Color selection is currently very confusing.  I think we may
+        # need to add another color selector for the hub label.  The current
+        # approach is to apply the specified color for the state to the hub label
+        # if the list of specified_state_index_items contains the value of i - 1
+        # since state indexes are zero based.
+        #cat("specified_state_index_items: ", specified_state_index_items, "\n");
+        #cat("length(specified_state_index_items): ", length(specified_state_index_items), "\n");
+        state_index = i - 1;
+        #cat("state_index: ", state_index, "\n");
+        if (state_index %in% specified_state_index_items) {
+            specified_state_color = specified_state_color_items[[i]];
+            #cat("specified_state_color: ", specified_state_color, "\n");
+            color = paste(c(col2rgb(specified_state_color)), collapse=",");
+            #cat("color 1: ", color, "\n");
+        } else {
+            color = paste(c(col2rgb("#FFFFFF")), collapse=",")
+            #cat("color 2: ", color, "\n");
+        }
         # Get the bigDataUrl.
         big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build);
         # trackDb.txt track hub entry.