[R] Circlize package: add text to chord in symmetric matrix

[Karim Mezhoud]

Dear All

temp matrix describes correlated genes by disease. Can I include which
genes are common between diseases in chord diagram?

> temp
      X1       X2    Disease1    Disease2    Disease3
1  Gene1 Disease1  1.00000000 -0.31428571  0.25714286
2  Gene2 Disease1  1.00000000  0.42857143  0.42857143
3  Gene3 Disease1  1.00000000 -0.60000000 -0.94285714
4  Gene4 Disease1  1.00000000 -0.54285714 -0.37142857
5  Gene5 Disease1  1.00000000  0.02857143  0.31428571
6  Gene1 Disease2 -0.31428571  1.00000000 -0.60000000
7  Gene2 Disease2  0.42857143  1.00000000  0.14285714
8  Gene3 Disease2 -0.60000000  1.00000000  0.71428571
9  Gene4 Disease2 -0.54285714  1.00000000  0.25714286
10 Gene5 Disease2  0.02857143  1.00000000  0.08571429
11 Gene1 Disease3  0.25714286 -0.60000000  1.00000000
12 Gene2 Disease3  0.42857143  0.14285714  1.00000000
13 Gene3 Disease3 -0.94285714  0.71428571  1.00000000
14 Gene4 Disease3 -0.37142857  0.25714286  1.00000000
15 Gene5 Disease3  0.31428571  0.08571429  1.00000000

The aggregation of temp gives:
temp1 <-aggregate(temp[,c(-1,-2)], list(temp[,2]), function(x) sum(x>.2))
rownames(temp1)<-temp1[,1]
temp1 <- temp1[,-1]

> temp1
         Disease1 Disease2 Disease3
Disease1        5        1        3
Disease2        1        5        2
Disease3        3        2        5

##plot chord diagram
chordDiagram(cor(temp1),symmetric = TRUE

Can I include which genes are common between diseases

##Mapping selected gene by disease
> tempGene1
      Disease1 Disease2 Disease3
Gene1        0        0        1
Gene2        0        1        1
Gene3        0        0        0
Gene4        0        0        0
Gene5        0        0        1

L <-apply(tempGene1,2,function(x) x[x==1])

> L
$Disease1
named integer(0)

$Disease2
Gene2
    1

$Disease3
Gene1 Gene2 Gene5
    1     1     1
Thanks
Karim

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