replace chr_num chr_name to chr

R/CALDER_hierarchy_v2.R

@@ -121,9 +121,6 @@
 
 		CALDER_CD_hierarchy_v2 = function(contact_tab_dump=NULL, contact_file_dump=NULL, contact_file_hic=NULL, chr, bin_size_input, bin_size2look, save_dir, save_intermediate_data=FALSE, swap_AB, ref_compartment_file, black_list_bins=NULL, feature_track=NULL)
 		{
-			chr_num = gsub('chr', '', chr, ignore.case=TRUE)
-			chr_name = paste0('chr', chr_num)
-
 		    get_cor_with_ref = function(chr_bin_pc, bin_size, ref_compartment_file=NULL, feature_track=NULL) ## correlation of PC1 with comp. domain rank of genome
 		    {
 		        ext_chr_bin_pc = function(chr_bin_pc) ## spand chr_bin_pc using 5kb bin
@@ -195,14 +192,12 @@
 		        {
 		        	colnames(feature_track) = c('chr', 'start', 'end', 'score')
 		        	feature_track$chr = gsub('chr', '', feature_track$chr)
-		        	feature_track_chr = feature_track[feature_track$chr==chr_num, ]
+		        	feature_track_chr = feature_track[feature_track$chr==chr, ]
 		        	ref_tab = get_binned_vals(feature_track_chr)
 		        }
 
 
-		        chr_name = gsub("chrchr", "chr", paste0("chr", ref_tab$chr))
-		        # chr_name = ifelse(chr_name=="chr23", "chrX", chr_name)
-		        ref_tab$chr = chr_name
+		        ref_tab$chr = chr
 		        colnames(ref_tab)[2] = "bin_index"
 
 		        ################################# convert chr_bin_pc into 5kb
@@ -218,14 +213,14 @@
 	    
 
 	        time0 = Sys.time()
-	        log_file = paste0(save_dir, '/chr', chr_num, '_log.txt')
-	        warning_file = paste0(save_dir, '/WARNING_chr', chr_num, '.txt')
+	        log_file = paste0(save_dir, '/', chr, '_log.txt')
+	        warning_file = paste0(save_dir, '/WARNING', chr, '.txt')
 	        cor_log_file = paste0(save_dir, '/cor_with_ref.txt')
 
 	        cat('>>>> Begin process contact matrix and compute correlation score at:', as.character(Sys.time()), '\n', file=log_file, append=FALSE)
 	        
 	        cat('[', as.character(chr),'] Begin process contact matrix and compute correlation score at:', as.character(Sys.time()), '\n')
-	        processed_data = contact_mat_processing_v2(contact_tab_dump, contact_file_dump=contact_file_dump, contact_file_hic=contact_file_hic, chr=chr_num, bin_size_input=bin_size_input, bin_size2look=bin_size2look, black_list_bins=black_list_bins)
+	        processed_data = contact_mat_processing_v2(contact_tab_dump, contact_file_dump=contact_file_dump, contact_file_hic=contact_file_hic, chr=chr, bin_size_input=bin_size_input, bin_size2look=bin_size2look, black_list_bins=black_list_bins)
 	     
 
 	        mat_dense = processed_data$mat_dense
@@ -279,7 +274,7 @@
 			## switch PC direction based on correlation with "ground_truth"	
 			{
 				initial_clusters_ori_bins = lapply(initial_clusters, function(v) as.numeric(bin_names[v]))
-				chr_bin_pc = data.table::data.table(chr=chr_name, bin=unlist(initial_clusters_ori_bins), PC1_val=rep(PC_12_atanh[,1], sapply(initial_clusters_ori_bins, length)))
+				chr_bin_pc = data.table::data.table(chr=chr, bin=unlist(initial_clusters_ori_bins), PC1_val=rep(PC_12_atanh[,1], sapply(initial_clusters_ori_bins, length)))
 				chr_bin_pc$start = (chr_bin_pc$bin - 1)*bin_size2look + 1
 				chr_bin_pc$end = chr_bin_pc$bin*bin_size2look
 
@@ -410,7 +405,7 @@
 
 		generate_hierachy_bed = function(chr, res, save_dir, bin_size)
 		{
-			chr_name = paste0('chr', chr)
+			chr_name = chr
 			# res = reses[[chr_name]][[CELL_LINE]]
 			hc = res$CALDER_hc