https://divingintogeneticsandgenomics.com/tags/matrix/ Recent content in Matrix on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Mon, 14 Apr 2014 13:54:00 -0700 https://divingintogeneticsandgenomics.com/archive/order-a-matrix-by-a-pre-defined-group-and-then-by-the-rowsums-in-r/ Mon, 14 Apr 2014 13:54:00 -0700 https://divingintogeneticsandgenomics.com/archive/order-a-matrix-by-a-pre-defined-group-and-then-by-the-rowsums-in-r/ I will lay down the R code below #create a matrix > mat<- matrix(sample.int(10, size=30, replace=T), ncol=3) > mat [,1] [,2] [,3] [1,] 4 7 6 [2,] 5 6 1 [3,] 4 3 1 [4,] 2 2 9 [5,] 4 5 4 [6,] 8 9 8 [7,] 5 9 7 [8,] 8 6 7 [9,] 3 8 5 [10,] 4 3 6 # column bind the mat and the sum of the rows together > mat1<- cbind(mat, rowSums(mat)) > mat1 [,1] [,2] [,3] [,4] [1,] 4 7 6 17 [2,] 5 6 1 12 [3,] 4 3 1 8 [4,] 2 2 9 13 [5,] 4 5 4 13 [6,] 8 9 8 25 [7,] 5 9 7 21 [8,] 8 6 7 21 [9,] 3 8 5 16 [10,] 4 3 6 13 # order the matrix by the rowSums(mat) > mat[order(rowSums(mat)),] [,1] [,2] [,3] [1,] 4 3 1 [2,] 5 6 1 [3,] 2 2 9 [4,] 4 5 4 [5,] 4 3 6 [6,] 3 8 5 [7,] 4 7 6 [8,] 5 9 7 [9,] 8 6 7 [10,] 8 9 8 # compare with the order by looking at the last column > mat1[order(rowSums(mat)),] [,1] [,2] [,3] [,4] [1,] 4 3 1 8 [2,] 5 6 1 12 [3,] 2 2 9 13 [4,] 4 5 4 13 [5,] 4 3 6 13 [6,] 3 8 5 16 [7,] 4 7 6 17 [8,] 5 9 7 21 [9,] 8 6 7 21 [10,] 8 9 8 25 # order the mat matrix in a decreasing order by adding a minus sign > mat[order(-rowSums(mat)),] [,1] [,2] [,3] [1,] 8 9 8 [2,] 5 9 7 [3,] 8 6 7 [4,] 4 7 6 [5,] 3 8 5 [6,] 2 2 9 [7,] 4 5 4 [8,] 4 3 6 [9,] 5 6 1 [10,] 4 3 1 # label the rows into different groups > rownames(mat)<- c("f","a","d","c","b","d","e","a","f","f") > mat [,1] [,2] [,3] f 4 7 6 a 5 6 1 d 4 3 1 c 2 2 9 b 4 5 4 d 8 9 8 e 5 9 7 a 8 6 7 f 3 8 5 f 4 3 6 > rownames(mat1)<- c("f","a","d","c","b","d","e","a","f","f") > mat1 [,1] [,2] [,3] [,4] f 4 7 6 17 a 5 6 1 12 d 4 3 1 8 c 2 2 9 13 b 4 5 4 13 d 8 9 8 25 e 5 9 7 21 a 8 6 7 21 f 3 8 5 16 f 4 3 6 13 > groups<- factor(rownames(mat)) > groups [1] f a d c b d e a f f Levels: a b c d e f # order the matrix by group first, and then within the subgroups, order by the rowSums > mat1[order(groups,rowSums(mat)),] [,1] [,2] [,3] [,4] a 5 6 1 12 a 8 6 7 21 b 4 5 4 13 c 2 2 9 13 d 4 3 1 8 d 8 9 8 25 e 5 9 7 21 f 4 3 6 13 f 3 8 5 16 f 4 7 6 17 It is extremely useful when I want to order the matrix by a pre-defined way and then plot the heatmap with heatmap2 in gplots package.