问题
I am able to follow the Circlize example in the description of the package on CRAN easily:
library('circlize')
set.seed(123)
mat = matrix(sample(1:100, 18, replace = TRUE), 3, 6)
rownames(mat) = letters[1:3]
colnames(mat) = LETTERS[1:6]
### basic settings
par(mfrow = c(3, 2))
par(mar = c(1, 1, 1, 1))
chordDiagram(mat)
however, when I replace mat with myMatrix I get this error:
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.
Can somebody explain why I am getting that message? I do not see a difference between mat and myMatrix other than myMatrix is larger:
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z A2 B2 C2 D2
A 1060360.659 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
B 0 32143148.75 996976.8445 0 4944648.524 5688385.041 61990.5913 0 0 0 0 -1563.225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31922242.6
C 0 0 6342776.843 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
D 0 0 0 28617385.81 17842142.64 0 0 0 0 0 0 0 0 409444.5633 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 4990921.202 105686446.3 536246.2188 0 0 0 0 0 0 0 8587899.583 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 378565.5746
F 0 92732.7741 0 4282.9319 33543553.89 36773976.59 1894761.93 0 0 333209.342 0 20739.0655 327956.7365 0 1022673.163 12229.0255 0 0 386112.1743 224039.3207 0 2395066.197 268247.2897 0 0 0 0 0 0 11926701.96
G 0 0 0 0 0 0 7753767.003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H 0 0 0 0 0 5184133.29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
I 0 0 0 0 462767.7374 0 0 0 8992223.296 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
J 0 0 0 0 0 0 0 0 0 1950552.642 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
K 0 0 0 0 891032.5584 0 0 0 0 0 520107.9821 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26724.8402 0 0 0 418902.5203
L 0 0 0 0 32044317.54 28147.5693 0 0 0 0 0 5383919.293 0 489912.5412 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4559115.003
M 0 0 0 0 0 3125823.41 0 0 0 0 0 0 1738293.164 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N 0 1053825.966 -8526.9758 1283429.314 60333051.34 2621812.931 -1130.1924 0 -779545.8004 8055145.684 918.8702 -379747.1919 -177.6205 298563606.5 -9316.8654 0 0 0 0 0 2631991.077 0 0 0 0 0 1107369.803 0 0 118812465
O 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500451.292 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7432418.396
P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Q 0 0 1496058.76 0 -4056617.74 294503 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 410.4 0 0 0 0 0 0 0 1765984767
Code
dd <- read.table(header = TRUE, text = " rn A B C D E F G H I J K L M N O P Q R S T U V W X Y Z A2 B2 C2 D2
A 1060360.659 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
B 0 32143148.75 996976.8445 0 4944648.524 5688385.041 61990.5913 0 0 0 0 -1563.225 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31922242.6
C 0 0 6342776.843 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
D 0 0 0 28617385.81 17842142.64 0 0 0 0 0 0 0 0 409444.5633 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 4990921.202 105686446.3 536246.2188 0 0 0 0 0 0 0 8587899.583 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 378565.5746
F 0 92732.7741 0 4282.9319 33543553.89 36773976.59 1894761.93 0 0 333209.342 0 20739.0655 327956.7365 0 1022673.163 12229.0255 0 0 386112.1743 224039.3207 0 2395066.197 268247.2897 0 0 0 0 0 0 11926701.96
G 0 0 0 0 0 0 7753767.003 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H 0 0 0 0 0 5184133.29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
I 0 0 0 0 462767.7374 0 0 0 8992223.296 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
J 0 0 0 0 0 0 0 0 0 1950552.642 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
K 0 0 0 0 891032.5584 0 0 0 0 0 520107.9821 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26724.8402 0 0 0 418902.5203
L 0 0 0 0 32044317.54 28147.5693 0 0 0 0 0 5383919.293 0 489912.5412 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4559115.003
M 0 0 0 0 0 3125823.41 0 0 0 0 0 0 1738293.164 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N 0 1053825.966 -8526.9758 1283429.314 60333051.34 2621812.931 -1130.1924 0 -779545.8004 8055145.684 918.8702 -379747.1919 -177.6205 298563606.5 -9316.8654 0 0 0 0 0 2631991.077 0 0 0 0 0 1107369.803 0 0 118812465
O 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500451.292 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7432418.396
P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Q 0 0 1496058.76 0 -4056617.74 294503 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 410.4 0 0 0 0 0 0 0 1765984767")
myMatrix <- as.matrix(dd[, -1])
rownames(myMatrix) <- dd[, 1]
chordDiagram(myMatrix)
回答1:
In the old version of circlize, the matrix must be of a matrix class instead of a data.frame, so you need to convert the data frame explicitly by:
myMatrix = as.matrix(A + B)
In circlize, a data frame is for data stored as a adjacency list (e.g the first column for group1, second column for group2, third column for the strength of the relation).
Since read.table() always returns a data.frame class, in the newer version of circlize, it is fine if the matrix represents as a data frame. When it is a data frame, the chordDiagram() will first check whether the number of columns is larger than 3 and all columns are numeric. If so, it will be converted to a matrix internally.
来源：https://stackoverflow.com/questions/35042752/r-circlize-error-in-circos-initialize