Changing order of elements on Chord diagram in R

Question

[Jonathan Yoou]

Hi all,

I'm currently making a Chort Diagram, and have no idea how to change the order of it.

Like showed on below picture, I want to change those two elements so that elements with grey colors are gathered together as they are from same group.

This is my code to make it:

set.seed(123) circos.clear() chordDiagram(input_mat, grid.col = color_grid.col, col = col_fun, annotationTrack = "grid", big.gap = 3, small.gap = 0.3, group = temp_group, symmetric = F, link.target.prop = F, preAllocateTracks = list( track.height = mm_h(3) ))

I've tried put "input_mat[wanted_order,wanted_order]" instead of "input_mat", but that doesn't work. Input_mat is a matrix; rownames and colnames are exactly same and values are count.

Does anyone have any idea?

[kalavattam]

It would be helpful if you provided a minimal reproducible example so others can test and troubleshoot your issue. Without knowing the structure/contents of input_mat, color_grid.col, col_fun, and temp_group, it’s difficult to determine why input_mat[wanted_order, wanted_order] isn’t working as you expect.

A small example with a dummy matrix and some mock values for the parameters would make it easier for people to play around with the code and suggest a fix. For example, something like this:

input_mat <- matrix(
    c(
        1, 2, 3, 4,
        # another row of numbers
        # another row of numbers
        # another row of numbers
    ),
nrow = 4, byrow = TRUE)

# Assign row and column names, and assign colors for groups, etc.

In case it helps, here’s a general guide on making an MRE: stackoverflow.com/help/minimal-reproducible-example.

Here's some info on formatting code on this site too: biostars.org/p/346537/#9584651.