Comments for the plotting function edited.

analyze_wvector.m

@@ -81,8 +81,8 @@
         jump_pos = j*max_dist;
         perfect_pos = start_pos + jump_pos;
         norms_pair_matrix(i+1,j+1) = norm( twoD_means(perfect_pos : perfect_pos + max_dist-1), 2);
-    end%inner for ends
-end%outer for ends
+    end % inner for ends
+end % outer for ends
 
 heatmapCSV_fname = strcat(folderName, '/weightVectorNormed_rank', num2str(rankId), '.csv');
 csvwrite(heatmapCSV_fname, norms_pair_matrix);

plotHeatmap.m

@@ -0,0 +1,57 @@
+function [plotDataM] = plotHeatmap(dataM, filename, climmin, climmax)
+
+% PLOTHEATMAP
+% Plots the heatmap given a matrix
+%
+% INPUT PARAMS
+% Param dataM
+% The matrix to be plotted
+%
+% Param filename
+% Filename for the PDF with the matrix plotted
+%
+% Param climmin, climmax
+% Colormap limits -- minimum and maximum
+% 
+% OUTPUT PARAMS
+% Param plotDataM
+%
+% ADDITIONAL NOTES
+% -- Standardize the values in the range [0,1]
+% -- Plot the heatmap
+%
+% Author: snikumbh@mpi-inf.mpg.de
+
+% instances along columns
+% sequences along rows
+
+shading interp;
+
+if nargin < 4
+    climmin = 0.75;
+    climmax = 0.95;
+elseif nargin < 2
+    filename = 'Heatmap.pdf';
+end
+
+%standardize matrix rows to range 0-to-1
+normDataM = standardizeMatrix(dataM);
+% plotDataM = normDataM;
+plotDataM = zeros(size(normDataM));
+% using rankings
+[~, rankingDataM] = sort(normDataM(1:size(dataM,1),1:size(dataM,2)), 2, 'descend');
+for i=1:size(plotDataM,1)
+    plotDataM(i,rankingDataM(i,:)) = 1:size(dataM,2);
+end
+%
+fig = figure;
+%
+clims = [climmin climmax];
+% clims = [0 1];
+imagesc(plotDataM);
+cb = colorbar;
+%
+% saveas(gcf, filename, 'pdf');
+print(gcf, filename, '-dpdf', '-r900');
+
+end

plot_heatmap.R

@@ -1,35 +1,39 @@
 
-#Reusing this R script from an earlier project.
+# Reusing this R script from an earlier project.
+# R script to plot a heatmap of the l2-normed weight vector
+#
+# Input: 
+# Input filename, output folder (path), rank of the weight vector, 
+# and the oligomer length for ODH
+#
+# Output: Weight vector l2-norm matrix heatmap
+#
+# Author: snikumbh@mpi-inf.mpg.de
 
-args <- commandArgs(TRUE) #send cellline, region#, oligoLen
-#send inputFilename outputFolder rank oligoLen
+args <- commandArgs(TRUE)
+# send inputFilename outputFolder rank and oligoLen
 inputFilename <- args[1]
 outputFolder <- args[2]
 rank <- args[3]
-#oligoLen <- 2
 oligoLen <- as.numeric(args[4])
-
+# this project, we only use the heatmap functionality
 plot_heatmap <- TRUE
 
 if(plot_heatmap == TRUE){
-
-library(lattice)
+    library(lattice)
     pdfname <- paste0(outputFolder, "/norms_mat_rank", rank, "_oligolen", oligoLen, ".pdf")
-    #print(PDF_FNAME)
     names <- seq(1,4^oligoLen, by=1)
     x <- expand.grid(rep(list(c('A', 'C', 'G', 'T')), 2))
     names <- do.call(paste0, rev(x))
     new.palette <- colorRampPalette(c("white","blue"),space="rgb")
-    fname <- inputFilename #paste0(a"all_weight_vectors/", cellline, "/heatmaps/norms_mat_run", runs[i], "_fold", folds[j] ,"_region", regions[r], "_oligolen", oligoLen, ".csv")
-    #print(fname)
+    fname <- inputFilename
     mat_data <- as.matrix(read.csv(fname, header = FALSE))
     rownames(mat_data) <- names
     colnames(mat_data) <- names
     pdf(pdfname)
     p <- levelplot(mat_data, col.regions=new.palette(20), scales=list(x=list(cex=.5, rot= 90),y=list(cex=.5)), xlab=list(label=paste0(oligoLen, "-mers"), cex=.9), ylab=list(label=paste0(oligoLen, "-mers"), cex=.9), region = TRUE, main="", title = paste0("_heatmaps"))
     print(p)
     dev.off()
-
 }else{
     pdf("barplot_max_weight_subvector.pdf")
     weights <- as.matrix(read.table("max_weight_subvector.lsv", sep = ",", header = FALSE), ncol = 1)