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plot_counts_matrix_log2_dist = function(matrix_file) {
data = read.table(file=matrix_file, com='', row.names=1, header=T)
conditions = colnames(data)
colors = rainbow(length(conditions))
plot(density(log2(data[,1])), col=colors[1], main=matrix_file, xlab='log2(frag_counts)', ylab='density')
for (i in 2:length(data[1,])) {
points(density(log2(data[,i])), type='l', col=colors[i])
}
legend('topright', conditions, col=colors, pch=15)
}
matrix_to_color_assignments = function(matrix_m, col=NULL, by=c("matrix", "row", "col")) {
if (! is.matrix(matrix_m))
stop("Error, matrix_to_color_assignments() requires a matrix as parameter.")
num_colors = 0
if (is.null(col)) {
num_colors = min(nrow(matrix_m), ncol(matrix_m))
col = rainbow(num_colors)
}
else {
num_colors = length(col)
}
by = match.arg(by)
if (by == "matrix") {
min_val = min(matrix_m, na.rm=T)
matrix_m = matrix_m - min_val
max_val = max(matrix_m, na.rm=T)
matrix_m = matrix_m / max_val * num_colors
#print(matrix_m)
matrix_m = apply(matrix_m, 1:2, function(x) ifelse (x<1, as.character(col[1]), as.character(col[x])));
matrix_m = matrix(as.character(matrix_m), nrow=dim(matrix_m)[1])
}
else {
row_or_col_only_color_selector_func = function(x) {
a = min(x, na.rm=T);
b = max(x, na.rm=T);
c = (x-a)/(b-a) * num_colors;
c = round(c);
c = ifelse (c<1, 1, c);
#print(paste(c("color selection: (a)", a, " (b)", b, " (c)", paste(c, sep=','))));
colors = as.character(col[c]);
return(colors);
}
if (by == "row") {
matrix_m = apply(matrix_m, 1, row_or_col_only_color_selector_func);
print(matrix_m)
print("dim matrix_m after apply"); print(dim(matrix_m))
matrix_m = t(matrix_m);
print("dim matrix_m after transpose: "); print(dim(matrix_m))
}
else {
# by column
matrix_m = apply(matrix_m, 2, row_or_col_only_color_selector_func);
}
}
#print(matrix_m)
return(matrix_m)
}
sample_matrix_to_color_assignments = function(sampleAnnotationsMatrix, colors) {
if (missing(colors))
colors = rainbow(nrow(sampleAnnotationsMatrix))
nsamples = nrow(sampleAnnotationsMatrix);
if (length(colors) < nrow(sampleAnnotationsMatrix))
stop("Error, only ", length(colors), " colors specified, but have ", nsamples, " samples");
for (i in 1:nrow(sampleAnnotationsMatrix)) {
c = colors[i]
sampleAnnotationsMatrix[i,] = sapply(sampleAnnotationsMatrix[i,], function(x) ifelse( x, as.character(c), 'white'))
}
return(sampleAnnotationsMatrix);
}
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