Fix colour.scheme() issues using input.colours in create.heatmap

[maotian06]

Here I want to show how to fix one colour.scheme issue in create.heatmap() function. Credit to @stefaneng for his smart solution:
The problem was about a duplicated color when I was trying to plot a collection of heatmaps using 10 different colors. With the old code:

isubgen.colours <- c(default.colours(num.clusters,'survival')[1:2],'gold3',default.colours(num.clusters,'survival')[4:num.clusters]);
plots <- list();
plot.idx <- 1;
for(i in 1:length(unique(iSubGen.class[,paste0('num_subtypes_',num.clusters)]))) {

	plots[[plot.idx]] <- create.heatmap(
		iSubGen.class[iSubGen.class[,paste0('num_subtypes_',num.clusters)] ==  i,rep(paste0('num_subtypes_',num.clusters),2)],
		same.as.matrix = TRUE,
		colour.scheme = isubgen.colours,
		at = seq(0.5,num.clusters+0.5),
		cluster.dimensions = 'none',
		print.colour.key = FALSE,
		xaxis.tck = 0,
		yaxis.tck = 0,
		colourkey.cex = 0.01,
		axes.lwd = 1,
		top.padding = 0,
		bottom.padding = 0,
		axis.xlab.padding = 0,
		covariates.top.padding = 0,
		right.padding = 0,
		left.padding = 0
		);
	plot.idx <- plot.idx + 1;
}
create.multipanelplot(
	plots,
        layout.width = 1,
	file = 'test.png'
);

It always shows a duplicated color at the end and the color doesn't match what the colour.scheme allocated:

@stefaneng 's solution was using the input.colours = TRUE option:

plots[[plot.idx]] <- create.heatmap(
		data.frame(rep(isubgen.colours[i],length(which(iSubGen.class[, paste0('num_subtypes_',num.clusters)] ==  i))),
					rep(isubgen.colours[i],length(which(iSubGen.class[, paste0('num_subtypes_',num.clusters)] ==  i)))),
		same.as.matrix = TRUE,
		input.colours = TRUE,
		clustering.method = 'none',
		print.colour.key = FALSE,
		xaxis.tck = 0,
		yaxis.tck = 0,
		colourkey.cex = 0.01,
		axes.lwd = 1,
		top.padding = 0,
		bottom.padding = 0,
		axis.xlab.padding = 0,
		covariates.top.padding = 0,
		right.padding = 0,
		left.padding = 0
		);

Problem resolved:

Not sure why.....

[stefaneng]

@maotian06 I like using input.colours = TRUE more but I think your first example is not working because you do no have total.colours = length(isubgen.colours) + 1? Not sure if this will fix it but I always have issues without setting total.colours