1. ggtree
  2. Commit 4d953959ed402af5cf3f1094190db782fb438f7a
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8ac2c857e0925891c1fcc68ee4e9869e4df05ccb

update add_colorbar



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103435 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 04/05/2015 13:23:10
Showing 5 changed files
NEWS
History View file @ 4d95395
... ... 
@@ -1,5 +1,6 @@
1 1 
 CHANGES IN VERSION 1.1.4
2 2 
 ------------------------
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+ o update add_colorbar to auto determine the position <2015-05-04, Mon>
3 4 
  o add_colorbar function <2015-04-30, Thu>
4 5
5 6 
 CHANGES IN VERSION 1.1.3
R/ggtree.R
History View file @ 4d95395
... ... 
@@ -390,13 +390,30 @@ expand <- function(tree_view, node) {
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 ##' @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) {
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     legend <- do.call("cbind", attr(color, "scale"))
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     legend[,1] <- round(as.numeric(legend[,1]), 2)
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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)]
R/tree.R
History View file @ 4d95395
... ... 
@@ -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)
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     df <- .assign_child_status(tr, df, yscale, yscale_mapping)
inst/examples/NAG_inHA1.txt
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... ... 
@@ -1,76 +1,151 @@
1 
-A/Swine/Binh_Duong/03_08/2010	6
2 
-A/Swine/Binh_Duong/03_10/2010	6
3 
-A/Swine/HK/2503/2011	7
4 
-A/Swine/HK_NS2439/2011	7
5 
-A/Swine/GX_NS2783/2010	7
6 
-A/Swine/GD/3767/2011	7
7 
-A/Swine/GX/2242/2011	7
8 
-A/Swine/GX/2803/2011	7
9 
-A/Swine/GX_NS3106/2011	7
10 
-A/Swine/GX_NS3108/2011	7
11 
-A/Swine/HK_NS2810/2011	7
12 
-A/Swine/HK/2857/2011	7
13 
-A/Swine/HK/3238/2011	7
14 
-A/Swine/HK/3700/2011	7
15 
-A/Swine/HK/168/2012	7
16 
-A/Swine/HK/459/2012	7
17 
-A/Swine/HK/1071/2012	7
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-A/Swine/HK/1284/2012	7
19 
-A/Swine/GX/650/2012	7
20 
-A/Swine/GX_NS1409/2012	8
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-A/Swine/GD/1599/2012	6
22 
-A/Swine/HK/2454/2012	7
23 
-A/Swine/GX/508/2012	7
24 
-A/Swine/HK_NS1651/2012	7
25 
-A/Swine/HK_NS2733/2012	7
26 
-A/Swine/HK/3280/2012	7
27 
-A/Swine/GX_NS2394/2012	7
28 
-A/Swine/GD_NS2701/2012	8
29 
-A/Swine/GD_NS2892/2012	8
30 
-A/Swine/GD/2919/2012	6
31 
-A/Swine/HK_NS2698/2012	8
32 
-A/Ho_Chi_Minh/459.6/2010	7
33 
-A/Netherlands/42/2006	10
34 
-A/Malaysia/29890/2004	11
35 
-A/New_York/334/2004	11
36 
-A/New_York/463/2005	11
37 
-A/New_York/238/2005	11
38 
-A/HaNoi/BM544/2004	10
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-A/Hong_Kong/HKU39/2004	11
40 
-A/Malaysia/29997/2004	10
41 
-A/Western_Australia/38/2003	10
42 
-A/Moscow/328/2003	11
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-A/Hanoi/BM767/2003	12
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-A/California/UR06-0589/2007	11
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-A/Brisbane/09/2006	11
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-A/Tokyo/Ut-Sk-1/2007	9
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-A/South_Carolina/NHRC0001/2006	11
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-A/Mexico/InDRE2160/2005	11
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-A/Colorado/UR06-0023/2007	11
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-A/Hong_Kong/NHRC0001/2005	11
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-A/California/NHRC0001/2005	11
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-A/Mexico/InDRE29/2006	11
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-A/California/VRDL165/2009	10
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-A/California/UR07-0017/2008	11
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-A/Ohio/UR07-0105/2008	10
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-A/Kyrgyzstan/WRAIR1255P/2008	11
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-A/Thailand/CU370/2008	11
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-A/Moscow/RII05/2012	11
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-A/Hokkaido/30-1-a/2013	12
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-A/Czech_Republic/119/2012	11
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-A/Petrozavodsk/RII01/2012	11
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-A/New_York/20342/2010	11
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-A/Boston/DOA52/2011	11
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-A/Czech_Republic/126/2012	11
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-A/Singapore/H2010.559C/2010	11
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-A/Auckland/615/2002	10
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-A/New_York/657/1994	9
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-A/Malaysia/12990/1999	11
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-A/HaNoi/1766/2001	11
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-A/Malaysia/10816/1999	11
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-A/Netherlands/126/2001	11
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-A/New_York/435/2000	11
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-A/New_York/452/1999	10
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-A/New_York/523/1998	10
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-A/New_York/582/1996	9
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-A/New_York/603/1996	9
1 
+A/Swine/Binh_Duong/03_08/2010	5
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+A/Swine/Binh_Duong/03_10/2010	5
3 
+A/Swine/HK/2503/2011	6
4 
+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/HK/3700/2011	6
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+A/Swine/HK/168/2012	6
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+A/Swine/HK/459/2012	6
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+A/Swine/HK/1071/2012	6
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+A/Swine/HK/1284/2012	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
24 
+A/Swine/HK_NS1651/2012	6
25 
+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
34 
+A/Malaysia/29890/2004	9
35 
+A/New_York/334/2004	9
36 
+A/New_York/463/2005	9
37 
+A/New_York/238/2005	9
38 
+A/HaNoi/BM544/2004	8
39 
+A/Hong_Kong/HKU39/2004	9
40 
+A/Malaysia/29997/2004	8
41 
+A/Western_Australia/38/2003	8
42 
+A/Moscow/328/2003	9
43 
+A/Hanoi/BM767/2003	9
44 
+A/California/UR06-0589/2007	9
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+A/Brisbane/09/2006	9
46 
+A/Tokyo/Ut-Sk-1/2007	7
47 
+A/South_Carolina/NHRC0001/2006	9
48 
+A/Mexico/InDRE2160/2005	9
49 
+A/Colorado/UR06-0023/2007	9
50 
+A/Hong_Kong/NHRC0001/2005	9
51 
+A/California/NHRC0001/2005	9
52 
+A/Mexico/InDRE29/2006	9
53 
+A/California/VRDL165/2009	8
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+A/California/UR07-0017/2008	9
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+A/Ohio/UR07-0105/2008	8
56 
+A/Kyrgyzstan/WRAIR1255P/2008	9
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+A/Thailand/CU370/2008	9
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+A/Moscow/RII05/2012	8
59 
+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
62 
+A/New_York/20342/2010	9
63 
+A/Boston/DOA52/2011	9
64 
+A/Czech_Republic/126/2012	9
65 
+A/Singapore/H2010.559C/2010	9
66 
+A/Auckland/615/2002	8
67 
+A/New_York/657/1994	7
68 
+A/Malaysia/12990/1999	9
69 
+A/HaNoi/1766/2001	9
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+A/Malaysia/10816/1999	9
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+A/Netherlands/126/2001	10
72 
+A/New_York/435/2000	9
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+A/New_York/452/1999	8
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+A/New_York/523/1998	9
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+A/New_York/582/1996	8
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+A/New_York/603/1996	8
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\ No newline at end of file
man/add_colorbar.Rd
History View file @ 4d95395
... ... 
@@ -4,7 +4,8 @@
4 4 
 \alias{add_colorbar}
5 5 
 \title{add_colorbar}
6 6 
 \usage{
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-add_colorbar(p, color, x, ymin, ymax, font.size = 4)
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+add_colorbar(p, color, x = NULL, ymin = NULL, ymax = NULL,
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+  font.size = 4)
8 9 
 }
9 10 
 \arguments{
10 11 
 \item{p}{tree view}