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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| Package: ComplexHeatmap | ||
| Type: Package | ||
| Title: Make Complex Heatmaps | ||
| Version: 2.3.2 | ||
| Date: 2020-03-05 | ||
| Version: 2.3.3 | ||
| Date: 2020-03-21 | ||
| Author: Zuguang Gu | ||
| Maintainer: Zuguang Gu <[email protected]> | ||
| Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,258 @@ | ||
| # `[.grob` = function(x, i) { | ||
| # x2 = x | ||
| # for(nm in SUBSETABLE_FIELDS[[ intersect(names(SUBSETABLE_FIELDS), class(x)) ]]) { | ||
| # if(inherits(x2[[nm]], "gpar")) { | ||
| # # change to the class defined here | ||
| # class(x2[[nm]]) = "gpar" | ||
| # } | ||
|
|
||
| # if(length(x2[[nm]]) > 1) { | ||
| # x2[[nm]] = x2[[nm]][i] | ||
| # } | ||
| # } | ||
| # x2 | ||
| # } | ||
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| # `[.gpar` = function(x, i) { | ||
| # lapply(x, function(y) { | ||
| # if(length(y) > 1) { | ||
| # y[i] | ||
| # } else { | ||
| # y | ||
| # } | ||
| # }) | ||
| # } | ||
|
|
||
| # SUBSETABLE_FIELDS = list( | ||
| # "text" = c("label", "x", "y", "gp"), | ||
| # "richtext_grob" = c("gp", "children", "childrenOrder") | ||
| # ) | ||
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||
| # length.text = function(x) { | ||
| # length(x$label) | ||
| # } | ||
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| # length.richtext_grob = function(x) { | ||
| # length(x$children) | ||
| # } | ||
|
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| # update_xy = function (gb, x, y, ...) { | ||
| # UseMethod("update_xy") | ||
| # } | ||
|
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||
| # update_xy.text = function(gb, x, y, ...) { | ||
| # n = length(gb$label) | ||
| # if(!missing(x)) { | ||
| # if(n > 1 & length(x) > 1 && n != length(x)) { | ||
| # stop_wrap("Length of `x` should be the same as the length of labels.") | ||
| # } | ||
| # gb$x = x | ||
| # } | ||
| # if(!missing(y)) { | ||
| # if(n > 1 & length(y) > 1 && n != length(y)) { | ||
| # stop_wrap("Length of `y` should be the same as the length of labels.") | ||
| # } | ||
| # gb$y = y | ||
| # } | ||
| # gb | ||
| # } | ||
|
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||
| # update_xy.richtext_grob = function(gb, x, y, ...) { | ||
| # n = length(gb$children) | ||
|
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||
| # if(!missing(x)) { | ||
| # if(n > 1 & length(x) > 1 && n != length(x)) { | ||
| # stop_wrap("Length of `x` should be the same as the length of labels.") | ||
| # } | ||
| # for(i in 1:n) { | ||
| # if(length(x) == 1) { | ||
| # gb$children[[i]]$vp$x = x | ||
| # } else { | ||
| # gb$children[[i]]$vp$x = x[i] | ||
| # } | ||
| # } | ||
| # } | ||
| # if(!missing(y)) { | ||
| # if(n > 1 & length(y) > 1 && n != length(y)) { | ||
| # stop_wrap("Length of `y` should be the same as the length of labels.") | ||
| # } | ||
| # for(i in 1:n) { | ||
| # if(length(y) == 1) { | ||
| # gb$children[[i]]$vp$y = y | ||
| # } else { | ||
| # gb$children[[i]]$vp$y = y[i] | ||
| # } | ||
| # } | ||
| # } | ||
| # gb | ||
| # } | ||
|
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||
| # textGrob = function(label, ...) { | ||
| # if(inherits(label, "grob")) { | ||
| # return(label) | ||
| # } else { | ||
| # grid::textGrob(label, ...) | ||
| # } | ||
| # } | ||
|
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||
| # grid.text = function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"), ...) { | ||
| # if(inherits(label, "grob")) { | ||
| # gb = label | ||
| # gb = update_xy(gb, x, y) | ||
| # grid.draw(gb) | ||
| # } else { | ||
| # grid::grid.text(label, x, y, ...) | ||
| # } | ||
| # } | ||
|
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||
| # == title | ||
| # Mark the text for the rendering by gridtext package | ||
| # | ||
| # == param | ||
| # -x Text labels. The value can be a vector. | ||
| # -... Other parameters passed to `gridtext::richtext_grob`. | ||
| # | ||
| # == details | ||
| # Text marked by `gt_render` will be rendered by `gridtext::richtext_grob` function. | ||
| # | ||
| # == example | ||
| # if(requireNamespace("gridtext")) { | ||
| # mat = matrix(rnorm(100), 10) | ||
| # rownames(mat) = letters[1:10] | ||
| # ht = Heatmap(mat, | ||
| # column_title = gt_render("Some <span style='color:blue'>blue text **in bold.**</span><br>And *italics text.*<br>And some <span style='font-size:18pt; color:black'>large</span> text.", r = unit(2, "pt"), padding = unit(c(2, 2, 2, 2), "pt")), | ||
| # column_title_gp = gpar(box_fill = "orange"), | ||
| # row_labels = gt_render(letters[1:10], padding = unit(c(2, 10, 2, 10), "pt")), | ||
| # row_names_gp = gpar(box_col = "red"), | ||
| # row_km = 2, | ||
| # row_title = gt_render(c("title1", "title2")), | ||
| # row_title_gp = gpar(box_fill = "yellow"), | ||
| # heatmap_legend_param = list( | ||
| # title = gt_render("<span style='color:orange'>**Legend title**</span>"), | ||
| # title_gp = gpar(box_fill = "grey"), | ||
| # at = c(-3, 0, 3), | ||
| # labels = gt_render(c("*negative* three", "zero", "*positive* three")) | ||
| # )) | ||
| # ht = rowAnnotation( | ||
| # foo = anno_text(gt_render(sapply(LETTERS[1:10], strrep, 10), align_widths = TRUE), | ||
| # gp = gpar(box_col = "blue", box_lwd = 2), | ||
| # just = "right", | ||
| # location = unit(1, "npc") | ||
| # )) + ht | ||
| # draw(ht) | ||
| # | ||
| # } | ||
| gt_render = function(x, ...) { | ||
| if(!requireNamespace("gridtext")) { | ||
| stop_wrap("gridtext package needs to be installed.") | ||
| } | ||
| param = list(...) | ||
| class(x) = "gridtext" | ||
| attr(x, "param") = param | ||
| return(x) | ||
| } | ||
|
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||
| # == title | ||
| # Subset method of gridtext class | ||
| # | ||
| # == param | ||
| # -x A vector of labels generated by `gt_render`. | ||
| # -index Index | ||
| # | ||
| # == details | ||
| # Internally used. | ||
| "[.gridtext" = function(x, index) { | ||
| cl = class(x) | ||
| param = attr(x, "param") | ||
| class(x) = NULL | ||
| x = x[index] | ||
| class(x) = cl | ||
| attr(x, "param") = param | ||
| x | ||
| } | ||
|
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||
| grid.text = function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"), ...) { | ||
| if(inherits(label, "gridtext")) { | ||
| # cat("draw text by gridtext:\n") | ||
| # print(label) | ||
| # cat("\n") | ||
| grid.draw(richtext_grob2(label, x, y, ...)) | ||
| } else { | ||
| grid::grid.text(label, x, y, ...) | ||
| } | ||
| } | ||
|
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||
| textGrob = function(label, ...) { | ||
| if(inherits(label, "gridtext")) { | ||
| richtext_grob2(label, ...) | ||
| } else { | ||
| grid::textGrob(label, ...) | ||
| } | ||
| } | ||
|
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||
| normalize_just = function(x) { | ||
| if(is.character(x)) { | ||
| x[x == "centre"] = "center" | ||
| if(identical(x, "center")) { | ||
| return(c(0.5, 0.5)) | ||
| } else if(identical(x, c("center", "center"))) { | ||
| return(c(0.5, 0.5)) | ||
| } else if(identical(x, c("left", "center"))) { | ||
| return(c(0, 0.5)) | ||
| } else if(identical(x, c("right", "center"))) { | ||
| return(c(1, 0.5)) | ||
| } else if(identical(x, c("center", "top"))) { | ||
| return(c(0.5, 1)) | ||
| } else if(identical(x, c("center", "bottom"))) { | ||
| return(c(0.5, 0)) | ||
| } else if(identical(x, c("left", "bottom"))) { | ||
| return(c(0, 0)) | ||
| } else if(identical(x, c("left", "top"))) { | ||
| return(c(0, 1)) | ||
| } else if(identical(x, c("right", "bottom"))) { | ||
| return(c(1, 0)) | ||
| } else if(identical(x, c("right", "top"))) { | ||
| return(c(1, 1)) | ||
| } else if(identical(x, c("left"))) { | ||
| return(c(0, 0.5)) | ||
| } else if(identical(x, c("right"))) { | ||
| return(c(1, 0.5)) | ||
| } else if(identical(x, c("bottom"))) { | ||
| return(c(0.5, 0)) | ||
| } else if(identical(x, c("top"))) { | ||
| return(c(0.5, 1)) | ||
| } | ||
| } | ||
| if(length(x) == 1) x = c(x, x) | ||
| return(x) | ||
| } | ||
|
|
||
| # argument from grid.text directly pass to richtext_grob, so some argument need | ||
| # to be adjusted, e.g. those not supported in richtext_grob | ||
| richtext_grob2 = function(label, ...) { | ||
| param0 = attr(label, "param") | ||
| param = list(text = label, ...) | ||
| for(nm in names(param0)) { | ||
| param[[nm]] = param0[[nm]] | ||
| } | ||
| if("just" %in% names(param)) { | ||
| j = normalize_just(param$just) | ||
| param$just = NULL | ||
| param$hjust = j[1] | ||
| param$vjust = j[2] | ||
| } | ||
| if("gp" %in% names(param)) { | ||
| gp = param$gp | ||
| l_box = grepl("^box_", names(gp)) | ||
| if(any(l_box)) { | ||
| box_gp = gp[l_box] | ||
| gp[l_box] = NULL | ||
| names(box_gp) = gsub("^box_", "", names(box_gp)) | ||
| class(gp) = "gpar" | ||
| class(box_gp) = "gpar" | ||
| param$gp = gp | ||
| param$box_gp = box_gp | ||
| } | ||
| } | ||
| do.call(gridtext::richtext_grob, param) | ||
| } |
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