I'm trying to reorder the rows and columns of an N*N matrix using a custom order in R.
The data matrix is:
structure(c(1, 0.43604, 0.09338, 0.4223, 0.18212, 0.50444, 0.00412,
-0.08552, 0.01674, 0.43604, 1, 0.36665, 0.32652, 0.00188, 0.39786,
-0.0802, -0.31283, -0.18666, 0.09338, 0.36665, 1, 0.58933, 0.09977,
0.39127, 0.03601, 0.00587, -0.44474, 0.4223, 0.32652, 0.58933,
1, 0.67113, 0.70805, 0.05161, 0.22738, -0.39247, 0.18212, 0.00188,
0.09977, 0.67113, 1, 0.73176, -0.04518, 0.30921, -0.08352, 0.50444,
0.39786, 0.39127, 0.70805, 0.73176, 1, -0.22003, -0.03522, -0.10815,
0.00412, -0.0802, 0.03601, 0.05161, -0.04518, -0.22003, 1, -0.01579,
-0.2002, -0.08552, -0.31283, 0.00587, 0.22738, 0.30921, -0.03522,
-0.01579, 1, 0.25466, 0.01674, -0.18666, -0.44474, -0.39247,
-0.08352, -0.10815, -0.2002, 0.25466, 1), .Dim = c(9L, 9L), .Dimnames = list(
c("MEOX2", "SNAI2", "TGIF1", "TCF3", "SOX4", "ZNF22", "RARA",
"ASCL1", "LHX2"), c("MEOX2", "SNAI2", "TGIF1", "TCF3", "SOX4",
"ZNF22", "RARA", "ASCL1", "LHX2")))
The code which I'm trying to use is:
order <- c("SNAI2","MEOX2","TGIF1","ASCL1","SOX4","ZNF22","LHX2","RARA","TCF2")
cormat_t_agg_GSE13041_GPL570_mapped<-reorder_mat(mat=data.matrix(cormat_t_agg_GSE13041_GPL570_mapped),order = order)
But I'm getting the same error even after making the necessary changes:
Error in reorder_mat(mat = data.matrix(cormat_t_agg_GSE13041_GPL570_mapped), :
The column names of the matrix you want to reorder must
be present in the vector 'order'
Although I've added a vector of the order this hasn't been working out well.
The error message describes it. Two possibilities:
in order, "TCF2" should be "TCF3"
in your correlation matrix, "TCF3" should be "TCF2"
Once you fix this name issue, you can do
cormat_t_agg_GSE13041_GPL570_mapped[order, order]