Create colored_Dots.R

[chasemc]

I am working on a visualization in one of my Shiny apps and needed circle representation of groups next to the dendrogram instead of bars; this may or may not be helpful to others.

[codecov-io]

Codecov Report

Merging #60 into master will decrease coverage by 0.93%. The diff coverage is 0%.

@@            Coverage Diff             @@
##           master      #60      +/-   ##
==========================================
- Coverage    38.6%   37.67%   -0.94%     
==========================================
  Files          49       51       +2     
  Lines        3898     3995      +97     
==========================================
  Hits         1505     1505              
- Misses       2393     2490      +97

Impacted Files	Coverage Δ
R/colored_Dots.R	0% <0%> (ø)
R/get_subdendrograms.R	0% <0%> (ø)

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[talgalili]

Thanks for the commit @chasemc Prior to accepting your commit two things are missing: 1) Could you add some roxygen documentation of the function? (you can use the sinew function makeOxygen to help you get the relevant structure). 2) would it be possible to add a unit test or two? (the package uses testthat)

If any of the two are difficult for you since you've never done them before, or if you don't have the time to do it, please just let me know. (I won't have time to do it in the near future, but at least I'll know that I need to do it later).

Thanks again, Tal

[chasemc]

Thanks, those are a little beyond me to be confident to do them correctly. This is 99% the code from your colored_bars(), except some modification the comments here:

if (horiz) {
      # Instead of rectangles, put in points at 1/2 x and y coordinates 
      #rect(-yb, xl, -yt, xr, col = as.character(C[, j]), 
      #     border = as.character(C[, j]))

      points((-yb+(-yt))/2,(xl+xr)/2,pch=19,col = as.character(C[, j]))

      par(srt = 90)
      if (is.null(rowLabels)) {
        s <- as.character(j)
        text(s, pos = 1, offset = 0.5, y = charHeight * 
               text_shift - rotated_str_dim(s)[2]/2, x = -(ystep * 
                                                             (j) * y_scale + y_shift), cex = cex.rowLabels)
      }
      else {
        s <- rowLabels[j]
        text(s, pos = 1, offset = 0.5, y = charHeight * 
               text_shift - rotated_str_dim(s)[2]/2, x = -(ystep * 
                                                             (j) * y_scale + y_shift), cex = cex.rowLabels)
      }
    }
    else {
      # Instead of rectangles, put in points at 1/2 x and y coordinates
      #rect(xl, yb, xr, yt, col = as.character(C[, j]), 
      #    border = as.character(C[, j]))
      points((xl1+xr)/2,(yb+yt)/2,pch=19,col = as.character(C[, j]))

[talgalili]

Hi @chasemc Could you please provide a simple example of how to use your function? Also, could you please explain what each of the argument means? (I can guess some of them, but if you could write this would help)

colors, dend, rowLabels = NULL, cex.rowLabels = 0.9, add = TRUE, y_scale, y_shift, text_shift = 1, sort_by_labels_order = TRUE, horiz = FALSE,

[chasemc]

Thanks for the patience, things are busy right now. But I'll make the example and roxygen as much as I can.

[talgalili]

Hi @chasemc Any news about this?

[chasemc]

Sorry, for having this hang around in your pull requests but I think it will be a nice addition as we're using it heavily within a Shiny app now (see pic). I've got the roxygen done and will be able to write the example(s) for it after my PhD preliminary exam next Wednesday (writing it will be a nice reprieve). Best, -Chase

[chasemc]

I was able to add Roxygen, as well as examples similar to "colored_bars". Unfortunately, I don't feel comfortable enough with testthat yet.

[talgalili]

Thanks. I'll try to look into it within the next week or so.