在 circlize 中绘制 chordDiagram 时出错:“Circos.initialize 中的错误" [英] Error when plotting chordDiagram in circlize: "Error in circos.initialize"
问题描述
当我尝试在 circlize (R) 中绘制 chordDiagram 时，出现持续性错误.我能够用一个数据集(Data1)很好地生成图，但不能用另一个(Data2)来生成图，它在结构上是相同的(据我所知).下面复制了两个数据集.它们具有相同的尺寸和结构——我想！'Year' 和 'month' 都被认为是具有相同级别数的因素，而 'mean' 是一个数字.两个数据集都被 R 识别为数据框.我一定遗漏了一些东西！
I am getting a persistent error when I attempt to plot a chordDiagram in circlize (R). I am able to generate the plot fine with one data set (Data1), but not with another (Data2), which is structurally identical (as far as I can tell). Both data sets are copied below. They have the same dimensions and structure - I think! 'Year' and 'month' are both recognised as factors with the same number of levels and 'mean' is a numeric. Both data sets are recognised as data frames by R. I must be missing something!
我得到的错误是:
错误在 circos.initialize(factors = factor(cate, levels = cate), xlim = cbind(rep(0, :由于xlim 是一个矩阵，所以它的行数应该与factors 的水平长度和列数相同."
The error I get is:
"Error in circos.initialize(factors = factor(cate, levels = cate), xlim = cbind(rep(0, :
Since xlim is a matrix, it should have same number of rows as the length of the level of factors and number of columns of 2."
我看过这篇帖子，但那里的解决方案没有帮帮我，所以我想我必须有一个不同的问题.....
I have seen this post, but the solution there didn't help me, so I think I must have a different issue.....
我使用的代码如下:
require(circlize)
数据框('Data1' 和 'Data2')在我的问题结束时被复制.
The data frames ('Data1' and 'Data2') are copied at the end of my question.
Data1 有效 - 生成的图没有错误:
Data1 works - the plots generate without error:
head(Data1)
Data1$Year <- as.factor(Data1$Year)
str(Data1)
# 'data.frame': 156 obs. of 3 variables:
# $ Year : Factor w/ 13 levels "2003","2004",..: 1 1 1 1 1 1 1 1 1 1 ...
# $ Month: Factor w/ 12 levels "Apr","Aug","Dec",..: 5 4 8 1 9 7 6 2 12 11.
# $ mean : num 0 0 0 0 0 ...
# Plot:
chordDiagram(Data1)
Data2 不绘制并给出错误
Data2 doesn't plot and gives the error
head(Data2)
Data2$Year <- as.factor(Data2$Year)
str(Data2)
# 'data.frame': 156 obs. of 3 variables:
# $ Year : Factor w/ 13 levels "2003","2004",..: 1 1 1 1 1 1 1 1 1 1 ...
# $ Month: Factor w/ 12 levels "Apr","Aug","Dec",..: 5 4 8 1 9 7 6 2 12 11
# $ mean : num 0 0 0 0 0 ...
# Plot
chordDiagram(Data2)
代码的第二部分，使用 Data2，产生:错误在 circos.initialize(factors = factor(cate, levels = cate), xlim = cbind(rep(0, :由于xlim 是一个矩阵，所以它的行数应该与factors 的级别长度和列数相同."
The second part of the code, using Data2, produces:
"Error in circos.initialize(factors = factor(cate, levels = cate), xlim = cbind(rep(0, :
Since xlim is a matrix, it should have same number of rows as the length of the level of factors and number of columns of 2."
如有任何建议，我们将不胜感激！
Any advice would be very gratefully received!
谢谢
数据 1:
Year Month mean
1 2003 Jan 0.00000000
2 2003 Feb 0.00000000
3 2003 Mar 0.00000000
4 2003 Apr 0.00000000
5 2003 May 0.00000000
6 2003 Jun 51.25480924
7 2003 Jul 52.86618015
8 2003 Aug 18.73057776
9 2003 Sep 30.78747020
10 2003 Oct 24.64436457
11 2003 Nov 65.18283156
12 2003 Dec 5.26012515
13 2004 Jan 4.54277226
14 2004 Feb 6.48744396
15 2004 Mar 18.51936027
16 2004 Apr 20.62421203
17 2004 May 10.52632961
18 2004 Jun 0.00000000
19 2004 Jul 2.07228430
20 2004 Aug 1.42555995
21 2004 Sep 0.00000000
22 2004 Oct 0.00000000
23 2004 Nov 0.00000000
24 2004 Dec 0.32547699
25 2005 Jan 1.66109048
26 2005 Feb 0.61855670
27 2005 Mar 3.44998035
28 2005 Apr 2.59668067
29 2005 May 0.36585366
30 2005 Jun 0.36258235
31 2005 Jul 6.59261048
32 2005 Aug 6.74112309
33 2005 Sep 3.26467331
34 2005 Oct 5.03515889
35 2005 Nov 12.43620184
36 2005 Dec 0.77694983
37 2006 Jan 0.00000000
38 2006 Feb 0.39627929
39 2006 Mar 0.77348066
40 2006 Apr 1.27516779
41 2006 May 0.11111111
42 2006 Jun 0.00000000
43 2006 Jul 11.54743590
44 2006 Aug 12.46652756
45 2006 Sep 8.53900709
46 2006 Oct 0.00000000
47 2006 Nov 2.87531133
48 2006 Dec 4.86021505
49 2007 Jan 0.74007156
50 2007 Feb 0.00000000
51 2007 Mar 0.60000000
52 2007 Apr 0.00000000
53 2007 May 0.53333333
54 2007 Jun 0.00000000
55 2007 Jul 4.36056332
56 2007 Aug 0.00000000
57 2007 Sep 3.72926026
58 2007 Oct 4.91828416
59 2007 Nov 7.32487797
60 2007 Dec 0.00000000
61 2008 Jan 5.88456083
62 2008 Feb 0.00000000
63 2008 Mar 1.14460094
64 2008 Apr 0.00000000
65 2008 May 0.00000000
66 2008 Jun 0.00000000
67 2008 Jul 0.00000000
68 2008 Aug 1.01011920
69 2008 Sep 2.61201413
70 2008 Oct 0.00000000
71 2008 Nov 0.00000000
72 2008 Dec 0.00000000
73 2009 Jan 5.74589612
74 2009 Feb 0.00000000
75 2009 Mar 2.42530066
76 2009 Apr 0.00000000
77 2009 May 2.28169014
78 2009 Jun 0.00000000
79 2009 Jul 3.37186343
80 2009 Aug 0.00000000
81 2009 Sep 9.67179487
82 2009 Oct 0.00000000
83 2009 Nov 4.00091324
84 2009 Dec 4.99561129
85 2010 Jan 0.00000000
86 2010 Feb 2.02962604
87 2010 Mar 0.11764706
88 2010 Apr 0.00000000
89 2010 May 1.38919826
90 2010 Jun 1.46666667
91 2010 Jul 0.47246377
92 2010 Aug 0.00000000
93 2010 Sep 0.00000000
94 2010 Oct 4.40459770
95 2010 Nov 0.00000000
96 2010 Dec 0.00000000
97 2011 Jan 0.40000000
98 2011 Feb 0.00000000
99 2011 Mar 0.00000000
100 2011 Apr 1.07972802
101 2011 May 0.00000000
102 2011 Jun 0.60277778
103 2011 Jul 10.82795699
104 2011 Aug 7.09462366
105 2011 Sep 1.24684685
106 2011 Oct 0.00000000
107 2011 Nov 3.65154853
108 2011 Dec 0.00000000
109 2012 Jan 1.28210424
110 2012 Feb 0.00000000
111 2012 Mar 1.77027890
112 2012 Apr 0.00000000
113 2012 May 2.00831169
114 2012 Jun 6.44055944
115 2012 Jul 11.02296928
116 2012 Aug 0.00000000
117 2012 Sep 9.22877123
118 2012 Oct 0.00000000
119 2012 Nov 2.37818182
120 2012 Dec 0.00000000
121 2013 Jan 2.34805195
122 2013 Feb 0.00000000
123 2013 Mar 0.00000000
124 2013 Apr 3.43796837
125 2013 May 2.79489914
126 2013 Jun 3.97525791
127 2013 Jul 17.69100716
128 2013 Aug 0.00000000
129 2013 Sep 24.65628317
130 2013 Oct 0.00000000
131 2013 Nov 6.90997527
132 2013 Dec 0.00000000
133 2014 Jan 0.00000000
134 2014 Feb 2.17611657
135 2014 Mar 0.77922078
136 2014 Apr 0.00000000
137 2014 May 2.05913758
138 2014 Jun 1.23313580
139 2014 Jul 2.17882118
140 2014 Aug 0.00000000
141 2014 Sep 1.55084316
142 2014 Oct 0.00000000
143 2014 Nov 0.77922078
144 2014 Dec 0.00000000
145 2015 Jan 0.00000000
146 2015 Feb 0.07633588
147 2015 Mar 0.00000000
148 2015 Apr 0.39958534
149 2015 May 1.95279500
150 2015 Jun 0.00000000
151 2015 Jul 6.69971250
152 2015 Aug 11.42582933
153 2015 Sep 11.28810414
154 2015 Oct 0.00000000
155 2015 Nov 3.97264445
156 2015 Dec 0.00000000
数据 2:
Year Month mean
1 2003 Jan 0.0000000
2 2003 Feb 0.0000000
3 2003 Mar 0.0000000
4 2003 Apr 0.0000000
5 2003 May 0.0000000
6 2003 Jun 0.0000000
7 2003 Jul 0.0000000
8 2003 Aug 0.0000000
9 2003 Sep 0.0000000
10 2003 Oct 2.2222222
11 2003 Nov 3.3333333
12 2003 Dec 17.7777778
13 2004 Jan 0.0000000
14 2004 Feb 0.0000000
15 2004 Mar 0.0000000
16 2004 Apr 1.1111111
17 2004 May 23.5609103
18 2004 Jun 42.2757697
19 2004 Jul 42.5814536
20 2004 Aug 29.6251673
21 2004 Sep 8.8888889
22 2004 Oct 4.4444444
23 2004 Nov 3.3333333
24 2004 Dec 3.3333333
25 2005 Jan 0.0000000
26 2005 Feb 0.0000000
27 2005 Mar 0.0000000
28 2005 Apr 0.0000000
29 2005 May 149.3280106
30 2005 Jun 6.6666667
31 2005 Jul 64.4444444
32 2005 Aug 18.8888889
33 2005 Sep 20.0000000
34 2005 Oct 7.7777778
35 2005 Nov 5.0000000
36 2005 Dec 2.2222222
37 2006 Jan 0.0000000
38 2006 Feb 0.0000000
39 2006 Mar 0.0000000
40 2006 Apr 0.0000000
41 2006 May 2.2222222
42 2006 Jun 66.6666667
43 2006 Jul 26.6666667
44 2006 Aug 25.5555556
45 2006 Sep 11.1111111
46 2006 Oct 4.4444444
47 2006 Nov 2.2222222
48 2006 Dec 17.7777778
49 2007 Jan 0.0000000
50 2007 Feb 0.0000000
51 2007 Mar 0.0000000
52 2007 Apr 0.0000000
53 2007 May 53.3333333
54 2007 Jun 36.6666667
55 2007 Jul 26.6666667
56 2007 Aug 0.0000000
57 2007 Sep 0.0000000
58 2007 Oct 0.0000000
59 2007 Nov 0.0000000
60 2007 Dec 0.0000000
61 2008 Jan 0.0000000
62 2008 Feb 0.0000000
63 2008 Mar 0.0000000
64 2008 Apr 0.0000000
65 2008 May 0.0000000
66 2008 Jun 0.0000000
67 2008 Jul 0.0000000
68 2008 Aug 0.0000000
69 2008 Sep 0.0000000
70 2008 Oct 0.0000000
71 2008 Nov 0.0000000
72 2008 Dec 0.0000000
73 2009 Jan 0.0000000
74 2009 Feb 0.0000000
75 2009 Mar 1.1111111
76 2009 Apr 9.4444444
77 2009 May 18.3333333
78 2009 Jun 18.8888889
79 2009 Jul 17.7777778
80 2009 Aug 22.2222222
81 2009 Sep 8.3333333
82 2009 Oct 13.8888889
83 2009 Nov 15.0000000
84 2009 Dec 13.8888889
85 2010 Jan 0.0000000
86 2010 Feb 0.0000000
87 2010 Mar 0.0000000
88 2010 Apr 0.0000000
89 2010 May 11.6666667
90 2010 Jun 17.2222222
91 2010 Jul 3.3333333
92 2010 Aug 0.0000000
93 2010 Sep 0.0000000
94 2010 Oct 0.0000000
95 2010 Nov 0.0000000
96 2010 Dec 0.0000000
97 2011 Jan 0.0000000
98 2011 Feb 0.0000000
99 2011 Mar 0.0000000
100 2011 Apr 5.9259259
101 2011 May 93.3333333
102 2011 Jun 10.3703704
103 2011 Jul 19.2592593
104 2011 Aug 14.8148148
105 2011 Sep 1.4814815
106 2011 Oct 3.7037037
107 2011 Nov 14.0740741
108 2011 Dec 11.8518519
109 2012 Jan 0.0000000
110 2012 Feb 0.0000000
111 2012 Mar 0.0000000
112 2012 Apr 184.4444444
113 2012 May 274.0740741
114 2012 Jun 37.0370370
115 2012 Jul 17.7777778
116 2012 Aug 0.0000000
117 2012 Sep 7.4074074
118 2012 Oct 12.5925926
119 2012 Nov 19.2592593
120 2012 Dec 28.8888889
121 2013 Jan 0.0000000
122 2013 Feb 0.0000000
123 2013 Mar 0.7407407
124 2013 Apr 1.4814815
125 2013 May 11.8518519
126 2013 Jun 62.2222222
127 2013 Jul 20.0000000
128 2013 Aug 33.3333333
129 2013 Sep 17.0370370
130 2013 Oct 0.0000000
131 2013 Nov 0.0000000
132 2013 Dec 0.0000000
133 2014 Jan 0.0000000
134 2014 Feb 0.0000000
135 2014 Mar 0.0000000
136 2014 Apr 0.0000000
137 2014 May 0.0000000
138 2014 Jun 0.0000000
139 2014 Jul 0.0000000
140 2014 Aug 0.0000000
141 2014 Sep 0.0000000
142 2014 Oct 0.0000000
143 2014 Nov 0.0000000
144 2014 Dec 0.0000000
145 2015 Jan 0.0000000
146 2015 Feb 0.0000000
147 2015 Mar 0.0000000
148 2015 Apr 0.0000000
149 2015 May 0.0000000
150 2015 Jun 0.0000000
151 2015 Jul 0.0000000
152 2015 Aug 0.0000000
153 2015 Sep 0.0000000
154 2015 Oct 0.0000000
155 2015 Nov 0.0000000
156 2015 Dec 0.0000000
推荐答案
我用 circlize 0.4.0(仅在 Github 上可用)尝试了两个数据集，并且都可以.我注意到在 Data2、Jan、Feb 和 Mar 中所有年份都为零，这可能会导致错误(这就像三个月从圆圈中删除，但我忘记在内部调整 xlim 中的行).最新版本已修复此问题，您可以通过devtools::install_github("jokergoo/circlize")更新.
I tried both datasets with circlize 0.4.0 (only available on Github) and both are OK. I noticed in Data2, Jan, Feb and Mar have zero in all years and that may cause the error (It is like the three months are removed from the circle but I forgot to adjust rows in xlim internally). This problem has been fixed in the newest version and you can update it by devtools::install_github("jokergoo/circlize").
这篇关于在 circlize 中绘制 chordDiagram 时出错:“Circos.initialize 中的错误"的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
