From d66f8fbe92720b8b5ad95cb74f735043802095b4 Mon Sep 17 00:00:00 2001 From: Pierre Ratinaud Date: Mon, 3 Nov 2014 09:38:26 +0100 Subject: [PATCH] ... --- Rscripts/Rgraph.R | 48 +++++++++++++++++++++++++----------------------- 1 file changed, 25 insertions(+), 23 deletions(-) diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R index 39fe618..14ce864 100644 --- a/Rscripts/Rgraph.R +++ b/Rscripts/Rgraph.R @@ -559,7 +559,7 @@ del.yellow <- function(colors) { tochange <- apply(rgbs, 2, is.yellow) tochange <- which(tochange) if (length(tochange)) { - gr.col <- grey.colors(length(tochange), start = 0.5) + gr.col <- grey.colors(length(tochange), start = 0.5, end = 0.8) } compt <- 1 for (val in tochange) { @@ -574,22 +574,23 @@ make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, le rain <- rainbow(clnb) compt <- 1 tochange <- NULL - for (my.color in rain) { - my.color <- col2rgb(my.color) - if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) { - tochange <- append(tochange, compt) - } - compt <- compt + 1 - } - if (!is.null(tochange)) { - gr.col <- grey.colors(length(tochange)) - compt <- 1 - for (val in tochange) { - rain[val] <- gr.col[compt] - compt <- compt + 1 - } - } - cl.color <- rain[classes] + #for (my.color in rain) { + # my.color <- col2rgb(my.color) + # if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) { + # tochange <- append(tochange, compt) + # } + # compt <- compt + 1 + #} + #if (!is.null(tochange)) { + # gr.col <- grey.colors(length(tochange)) + # compt <- 1 + # for (val in tochange) { + # rain[val] <- gr.col[compt] + # compt <- compt + 1 + # } + #} + rain <- del.yellow(rain) + cl.color <- rain[classes] if (black) { cl.color <- 'black' } @@ -637,8 +638,9 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro vec.mat[3,] <- 3:(length(sum.cl)+2) layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(2,1,6)) if (! bw) { - col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)] + col <- rainbow(length(sum.cl)) col <- del.yellow(col) + col <- col[as.numeric(tree$tip.label)] colcloud <- rainbow(length(sum.cl)) colcloud <- del.yellow(colcloud) } @@ -658,7 +660,7 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro #wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(1.5, 0.2), random.order=FALSE, colors = colcloud[i]) yval <- 1.1 plot(0,0,pch='', axes = FALSE) - vcex <- norm.vec(lclasses[[i]], 1.5, 2.5) + vcex <- norm.vec(lclasses[[i]], 1.5, 1.5) for (j in 1:length(lclasses[[i]])) { yval <- yval-(strheight( names(lclasses[[i]])[j],cex=vcex[j])+0.02) text(-0.9, yval, names(lclasses[[i]])[j], cex = vcex[j], col = colcloud[i], adj=0) @@ -796,15 +798,15 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2 par(mar=c(0,0,0,0)) if (!is.null(classes)) { matlay <- matrix(c(1,2,3,4),1,byrow=TRUE) - lay.width <- c(3,1,3,2) + lay.width <- c(3,2,3,2) } else { matlay <- matrix(c(1,2,3),1,byrow=TRUE) } layout(matlay, widths=lay.width,TRUE) - par(mar=c(3,0,2,0),cex=1) + par(mar=c(3,0,2,4),cex=1) label.ori<-tree[[2]] if (!is.null(lab)) { - tree$tip.label <- lab + tree$tip.label <- lab[tree.order] } else { tree[[2]]<-paste('classe ',tree[[2]]) } @@ -823,7 +825,7 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2 col.bars <- grey.colors(nrow(to.plot),0,0.8) } col <- col[tree.order] - plot.phylo(tree,label.offset=0.1,tip.col=col) + plot.phylo(tree,label.offset=0.2,tip.col=col) if (!is.null(classes)) { par(cex=0.7) par(mar=c(3,0,2,1)) -- 2.7.4