Commit id: 8ac2c857e0925891c1fcc68ee4e9869e4df05ccb
update add_colorbar
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103435 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -390,13 +390,30 @@ expand <- function(tree_view, node) { |
390 | 390 |
##' @export |
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##' @importFrom ggplot2 annotate |
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##' @author Guangchuang Yu |
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-add_colorbar <- function(p, color, x, ymin, ymax, font.size=4) { |
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+add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) { |
|
394 | 394 |
legend <- do.call("cbind", attr(color, "scale")) |
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|
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legend[,1] <- round(as.numeric(legend[,1]), 2) |
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|
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## legend[nrow(legend),1] <- paste(">=", legend[nrow(legend),1]) |
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- |
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+ |
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+ if (is.null(x)) { |
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+ xx <- range(p$data$x) |
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+ x <- min(xx)+diff(xx)/100 |
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+ } |
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+ |
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+ yy <- range(p$data$y) |
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+ if (is.null(ymin)) { |
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+ if (is.null(ymax)) { |
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+ ymax <- max(yy) - diff(yy)/100 |
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+ } |
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+ ymin <- ymax - diff(yy)/15 |
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+ } |
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+ |
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+ if (is.null(ymax)) { |
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+ ymax <- ymin + diff(yy)/15 |
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+ } |
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+ |
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yy <- seq(ymin, ymax, length.out=nrow(legend)+1) |
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ymin <- yy[1:nrow(legend)] |
... | ... |
@@ -765,6 +765,14 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) { |
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stop("yscale_mapping should be a named numeric vector...") |
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} |
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+ if (yscale == "label") { |
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+ yy <- df[, yscale] |
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+ ii <- which(is.na(yy)) |
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+ if (length(ii)) { |
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+ df[ii, yscale] <- df[ii, "node"] |
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+ } |
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+ } |
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+ |
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## assign to parent status is more prefer... |
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df <- .assign_parent_status(tr, df, yscale) |
770 | 778 |
df <- .assign_child_status(tr, df, yscale, yscale_mapping) |
... | ... |
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+A/Swine/Binh_Duong/03_08/2010 5 |
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+A/Swine/Binh_Duong/03_10/2010 5 |
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+A/Swine/HK/2503/2011 6 |
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+A/Swine/HK_NS2439/2011 6 |
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+A/Swine/GX_NS2783/2010 6 |
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+A/Swine/GD/3767/2011 6 |
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+A/Swine/GX/2242/2011 6 |
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+A/Swine/GX/2803/2011 6 |
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+A/Swine/GX_NS3106/2011 6 |
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+A/Swine/GX_NS3108/2011 6 |
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+A/Swine/HK_NS2810/2011 6 |
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+A/Swine/HK/2857/2011 6 |
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+A/Swine/HK/3238/2011 6 |
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+A/Swine/GX/650/2012 6 |
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+A/Swine/GX_NS1409/2012 6 |
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+A/Swine/GD/1599/2012 5 |
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+A/Swine/HK/2454/2012 6 |
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+A/Swine/GX/508/2012 6 |
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+A/Swine/HK_NS1651/2012 6 |
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+A/Swine/HK_NS2733/2012 6 |
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+A/Swine/HK/3280/2012 6 |
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+A/Swine/GX_NS2394/2012 6 |
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+A/Swine/GD_NS2701/2012 6 |
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+A/Swine/GD_NS2892/2012 6 |
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+A/Swine/GD/2919/2012 5 |
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+A/Swine/HK_NS2698/2012 6 |
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+A/Ho_Chi_Minh/459.6/2010 6 |
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+A/Netherlands/42/2006 8 |
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+A/Malaysia/29890/2004 9 |
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+A/New_York/334/2004 9 |
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+A/New_York/463/2005 9 |
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+A/New_York/238/2005 9 |
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+A/HaNoi/BM544/2004 8 |
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+A/Hong_Kong/HKU39/2004 9 |
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+A/Malaysia/29997/2004 8 |
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+A/Western_Australia/38/2003 8 |
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+A/Moscow/328/2003 9 |
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+A/Hanoi/BM767/2003 9 |
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+A/California/UR06-0589/2007 9 |
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+A/Brisbane/09/2006 9 |
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+A/Tokyo/Ut-Sk-1/2007 7 |
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+A/South_Carolina/NHRC0001/2006 9 |
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+A/Mexico/InDRE2160/2005 9 |
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+A/Hong_Kong/NHRC0001/2005 9 |
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+A/Moscow/RII05/2012 8 |
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+A/Hokkaido/30-1-a/2013 8 |
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+A/Czech_Republic/119/2012 8 |
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+A/Petrozavodsk/RII01/2012 8 |
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+A/Czech_Republic/126/2012 9 |
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