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

... ...
@@ -1,5 +1,6 @@
1 1
 CHANGES IN VERSION 1.1.4
2 2
 ------------------------
3
+ 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
... ...
@@ -390,13 +390,30 @@ expand <- function(tree_view, node) {
390 390
 ##' @export
391 391
 ##' @importFrom ggplot2 annotate
392 392
 ##' @author Guangchuang Yu
393
-add_colorbar <- function(p, color, x, ymin, ymax, font.size=4) {
393
+add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {
394 394
     legend <- do.call("cbind", attr(color, "scale"))
395 395
     
396 396
     legend[,1] <- round(as.numeric(legend[,1]), 2)
397 397
     
398 398
     ## legend[nrow(legend),1] <- paste(">=", legend[nrow(legend),1])
399
-    
399
+
400
+    if (is.null(x)) {
401
+        xx <- range(p$data$x)
402
+        x <- min(xx)+diff(xx)/100
403
+    }
404
+
405
+    yy <- range(p$data$y)
406
+    if (is.null(ymin)) {
407
+        if (is.null(ymax)) {        
408
+            ymax <- max(yy) - diff(yy)/100
409
+        }
410
+        ymin <- ymax - diff(yy)/15
411
+    }
412
+
413
+    if (is.null(ymax)) {
414
+        ymax <- ymin + diff(yy)/15
415
+    }
416
+        
400 417
     yy <- seq(ymin, ymax, length.out=nrow(legend)+1)
401 418
 
402 419
     ymin <- yy[1:nrow(legend)]
... ...
@@ -765,6 +765,14 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {
765 765
         stop("yscale_mapping should be a named numeric vector...")
766 766
     }
767 767
 
768
+    if (yscale == "label") {
769
+        yy <- df[, yscale]
770
+        ii <- which(is.na(yy))
771
+        if (length(ii)) {
772
+            df[ii, yscale] <- df[ii, "node"]
773
+        }
774
+    }
775
+    
768 776
     ## assign to parent status is more prefer...
769 777
     df <- .assign_parent_status(tr, df, yscale)
770 778
     df <- .assign_child_status(tr, df, yscale, yscale_mapping)
... ...
@@ -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
18
-A/Swine/HK/1284/2012	7
19
-A/Swine/GX/650/2012	7
20
-A/Swine/GX_NS1409/2012	8
21
-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
39
-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
43
-A/Hanoi/BM767/2003	12
44
-A/California/UR06-0589/2007	11
45
-A/Brisbane/09/2006	11
46
-A/Tokyo/Ut-Sk-1/2007	9
47
-A/South_Carolina/NHRC0001/2006	11
48
-A/Mexico/InDRE2160/2005	11
49
-A/Colorado/UR06-0023/2007	11
50
-A/Hong_Kong/NHRC0001/2005	11
51
-A/California/NHRC0001/2005	11
52
-A/Mexico/InDRE29/2006	11
53
-A/California/VRDL165/2009	10
54
-A/California/UR07-0017/2008	11
55
-A/Ohio/UR07-0105/2008	10
56
-A/Kyrgyzstan/WRAIR1255P/2008	11
57
-A/Thailand/CU370/2008	11
58
-A/Moscow/RII05/2012	11
59
-A/Hokkaido/30-1-a/2013	12
60
-A/Czech_Republic/119/2012	11
61
-A/Petrozavodsk/RII01/2012	11
62
-A/New_York/20342/2010	11
63
-A/Boston/DOA52/2011	11
64
-A/Czech_Republic/126/2012	11
65
-A/Singapore/H2010.559C/2010	11
66
-A/Auckland/615/2002	10
67
-A/New_York/657/1994	9
68
-A/Malaysia/12990/1999	11
69
-A/HaNoi/1766/2001	11
70
-A/Malaysia/10816/1999	11
71
-A/Netherlands/126/2001	11
72
-A/New_York/435/2000	11
73
-A/New_York/452/1999	10
74
-A/New_York/523/1998	10
75
-A/New_York/582/1996	9
76
-A/New_York/603/1996	9
1
+A/Swine/Binh_Duong/03_08/2010	5
2
+A/Swine/Binh_Duong/03_10/2010	5
3
+A/Swine/HK/2503/2011	6
4
+A/Swine/HK_NS2439/2011	6
5
+A/Swine/GX_NS2783/2010	6
6
+A/Swine/GD/3767/2011	6
7
+A/Swine/GX/2242/2011	6
8
+A/Swine/GX/2803/2011	6
9
+A/Swine/GX_NS3106/2011	6
10
+A/Swine/GX_NS3108/2011	6
11
+A/Swine/HK_NS2810/2011	6
12
+A/Swine/HK/2857/2011	6
13
+A/Swine/HK/3238/2011	6
14
+A/Swine/HK/3700/2011	6
15
+A/Swine/HK/168/2012	6
16
+A/Swine/HK/459/2012	6
17
+A/Swine/HK/1071/2012	6
18
+A/Swine/HK/1284/2012	6
19
+A/Swine/GX/650/2012	6
20
+A/Swine/GX_NS1409/2012	6
21
+A/Swine/GD/1599/2012	5
22
+A/Swine/HK/2454/2012	6
23
+A/Swine/GX/508/2012	6
24
+A/Swine/HK_NS1651/2012	6
25
+A/Swine/HK_NS2733/2012	6
26
+A/Swine/HK/3280/2012	6
27
+A/Swine/GX_NS2394/2012	6
28
+A/Swine/GD_NS2701/2012	6
29
+A/Swine/GD_NS2892/2012	6
30
+A/Swine/GD/2919/2012	5
31
+A/Swine/HK_NS2698/2012	6
32
+A/Ho_Chi_Minh/459.6/2010	6
33
+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
45
+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
54
+A/California/UR07-0017/2008	9
55
+A/Ohio/UR07-0105/2008	8
56
+A/Kyrgyzstan/WRAIR1255P/2008	9
57
+A/Thailand/CU370/2008	9
58
+A/Moscow/RII05/2012	8
59
+A/Hokkaido/30-1-a/2013	8
60
+A/Czech_Republic/119/2012	8
61
+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
70
+A/Malaysia/10816/1999	9
71
+A/Netherlands/126/2001	10
72
+A/New_York/435/2000	9
73
+A/New_York/452/1999	8
74
+A/New_York/523/1998	9
75
+A/New_York/582/1996	8
76
+A/New_York/603/1996	8
77
+77	8
78
+78	8
79
+79	8
80
+80	8
81
+81	8
82
+82	8
83
+83	9
84
+84	9
85
+85	9
86
+86	9
87
+87	9
88
+88	9
89
+89	9
90
+90	9
91
+91	9
92
+92	9
93
+93	9
94
+94	9
95
+95	9
96
+96	9
97
+97	9
98
+98	9
99
+99	9
100
+100	9
101
+101	9
102
+102	9
103
+103	9
104
+104	9
105
+105	9
106
+106	9
107
+107	9
108
+108	9
109
+109	9
110
+110	9
111
+111	9
112
+112	9
113
+113	9
114
+114	8
115
+115	8
116
+116	8
117
+117	9
118
+118	6
119
+119	5
120
+120	6
121
+121	6
122
+122	6
123
+123	6
124
+124	6
125
+125	6
126
+126	6
127
+127	6
128
+128	6
129
+129	6
130
+130	6
131
+131	6
132
+132	6
133
+133	6
134
+134	6
135
+135	6
136
+136	6
137
+137	6
138
+138	6
139
+139	6
140
+140	6
141
+141	6
142
+142	6
143
+143	6
144
+144	6
145
+145	6
146
+146	6
147
+147	6
148
+148	6
149
+149	9
150
+150	9
151
+151	8
77 152
\ No newline at end of file
... ...
@@ -4,7 +4,8 @@
4 4
 \alias{add_colorbar}
5 5
 \title{add_colorbar}
6 6
 \usage{
7
-add_colorbar(p, color, x, ymin, ymax, font.size = 4)
7
+add_colorbar(p, color, x = NULL, ymin = NULL, ymax = NULL,
8
+  font.size = 4)
8 9
 }
9 10
 \arguments{
10 11
 \item{p}{tree view}