Fixed pch matrix reordering by:
For column, move reording out of for loop, so matrix is only reordered once.
For row, added reordering in before for loop.
Also changed some indentation.
mbdabrowska1 authored on 13/08/2019 10:20:26 • GitHub committed on 13/08/2019 10:20:26 | ... | ... |
@@ -222,33 +222,38 @@ anno_simple = function(x, col, na_col = "grey", |
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row_fun = function(index) {
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- n = length(index) |
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- y = (n - seq_len(n) + 0.5) / n |
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- if(is.matrix(value)) {
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- nc = ncol(value) |
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- for(i in seq_len(nc)) {
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- fill = map_to_colors(color_mapping, value[index, i]) |
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- grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, |
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- gp = do.call("gpar", c(list(fill = fill), gp)))
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- if(!is.null(pch)) {
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- l = !is.na(pch[, i]) |
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- grid.points(x = rep((i-0.5)/nc, sum(l)), y = y[l], pch = pch[l, i], |
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- size = {if(length(pt_size) == 1) pt_size else pt_size[i]},
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- gp = subset_gp(pt_gp, i)) |
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- } |
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- } |
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- } else {
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- fill = map_to_colors(color_mapping, value[index]) |
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- grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
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- if(!is.null(pch)) {
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- pch = pch[index] |
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- pt_size = pt_size[index] |
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- pt_gp = subset_gp(pt_gp, index) |
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- l = !is.na(pch) |
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- grid.points(x = rep(0.5, sum(l)), y = y[l], pch = pch[l], size = pt_size[l], |
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- gp = subset_gp(pt_gp, which(l))) |
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- } |
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- } |
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+ n = length(index) |
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+ y = (n - seq_len(n) + 0.5) / n |
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+ if(is.matrix(value)) {
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+ nc = ncol(value) |
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+ if(is.matrix(pch)){
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+ pch = pch[index, , drop = FALSE] |
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+ } else if(is.vector(pch)) {
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+ stop_wrap(paste0("Since annotation is a matrix, pch should also be a matrix")
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+ } |
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+ for(i in seq_len(nc)) {
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+ fill = map_to_colors(color_mapping, value[index, i]) |
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+ grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, |
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+ gp = do.call("gpar", c(list(fill = fill), gp)))
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+ if(!is.null(pch)) {
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+ l = !is.na(pch[, i]) |
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+ grid.points(x = rep((i-0.5)/nc, sum(l)), y = y[l], pch = pch[l, i], |
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+ size = {if(length(pt_size) == 1) pt_size else pt_size[i]},
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+ gp = subset_gp(pt_gp, i)) |
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+ } |
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+ } |
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+ } else {
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+ fill = map_to_colors(color_mapping, value[index]) |
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+ grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
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+ if(!is.null(pch)) {
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+ pch = pch[index] |
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+ pt_size = pt_size[index] |
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+ pt_gp = subset_gp(pt_gp, index) |
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+ l = !is.na(pch) |
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+ grid.points(x = rep(0.5, sum(l)), y = y[l], pch = pch[l], size = pt_size[l], |
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+ gp = subset_gp(pt_gp, which(l))) |
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+ } |
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+ } |
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if(border) grid.rect(gp = gpar(fill = "transparent")) |
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} |
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| ... | ... |
@@ -258,28 +263,34 @@ anno_simple = function(x, col, na_col = "grey", |
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x = (seq_len(n) - 0.5) / n |
| 259 | 264 |
if(is.matrix(value)) {
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nc = ncol(value) |
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+ |
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+ if(is.matrix(pch)){
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+ pch = pch[index, , drop = FALSE] |
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+ } else if(is.vector(pch)) {
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+ stop_wrap(paste0("Since annotation is a matrix, pch should also be a matrix")
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+ } |
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+ |
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for(i in seq_len(nc)) {
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fill = map_to_colors(color_mapping, value[index, i]) |
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grid.rect(x, y = (nc-i +0.5)/nc, width = 1/n, height = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))
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- if(!is.null(pch)) {
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- pch = pch[index, , drop = FALSE] |
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- l = !is.na(pch[, i]) |
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- grid.points(x[l], y = rep((nc-i +0.5)/nc, sum(l)), pch = pch[l, i], |
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- size = {if(length(pt_size) == 1) pt_size else pt_size[i]},
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- gp = subset_gp(pt_gp, i)) |
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- } |
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- } |
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+ if(!is.null(pch)){
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+ l = !is.na(pch[, i]) |
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+ grid.points(x[l], y = rep((nc-i +0.5)/nc, sum(l)), pch = pch[l, i], |
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+ size = {if(length(pt_size) == 1) pt_size else pt_size[i]},
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+ gp = subset_gp(pt_gp, i)) |
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+ } |
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+ } |
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} else {
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- fill = map_to_colors(color_mapping, value[index]) |
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- grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
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- if(!is.null(pch)) {
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- pch = pch[index] |
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- pt_size = pt_size[index] |
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- pt_gp = subset_gp(pt_gp, index) |
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- l = !is.na(pch) |
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- grid.points(x[l], y = rep(0.5, sum(l)), pch = pch[l], size = pt_size[l], |
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- gp = subset_gp(pt_gp, which(l))) |
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- } |
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+ fill = map_to_colors(color_mapping, value[index]) |
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+ grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
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+ if(!is.null(pch)) {
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+ pch = pch[index] |
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+ pt_size = pt_size[index] |
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+ pt_gp = subset_gp(pt_gp, index) |
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+ l = !is.na(pch) |
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+ grid.points(x[l], y = rep(0.5, sum(l)), pch = pch[l], size = pt_size[l], |
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+ gp = subset_gp(pt_gp, which(l))) |
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+ } |
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} |
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if(border) grid.rect(gp = gpar(fill = "transparent")) |
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} |