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Dev 202403 #9

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@russHyde russHyde commented Mar 12, 2024 •
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This PR contains code for reformatting the dendrogram and heatmap figures that are produced by tfpscanner. The aims are:

  • make the colour scheme of the dendrogram more sensible (with a neutral colour for midpoints of the statistics; and a diverging palette)
  • make the colour scheme for the heatmap more neutral - so it doesn't clash with the informative colours in the dendrogram
  • ensure the dendrogram and heatmap don't overlap (or at least, provide the user a way to modify the figures so that they don't overlap)
  • condense the legends for the figures.

In addition, we fixed a few minor issues:

  • the README now mentions using create_browser_data(), rather than the non-existing create_browser_files()
  • All warnings arising during R CMD check have been fixed
  • The lintr config has been updated because it previously referred to a function that lintr no longer exports
  • The package passes linting

@russHyde russHyde marked this pull request as draft March 12, 2024 10:07
russHyde and others added 17 commits March 19, 2024 11:44
@russHyde
bump CI scripts to use R 4.3 and bioconductor 3.18
c79e1b2
@russHyde
Merge pull request #29 from jumpingrivers/fix-ci
93b346f 
bump CI scripts to use R 4.3 and bioconductor 3.18
@russHyde
remove legend for internal-node vs leaf 'shape' aesthetic
70e7518
@russHyde
feat: squash genotype TRUE/FALSE legend levels into 1 column
75b41a5
@russHyde
feat: user can set heatmap_offset (so heatmap doesn't overlap tree)
7cfd9f0
@russHyde
feat: make heatmap colours light/mid grey instead of colourful
942de42
@russHyde
doc: inherit heatmap parameters from treeview() in all downstream fun…
863ecc1 
…ction docs
@russHyde
Merge pull request #26 from jumpingrivers/fix-heatmap
b004d49 
Fix heatmap
@russHyde
feat: define colours for dendrogram branches in treeview() args; Use …
97ca176 
…Blue-Red diverging palette with light-grey midpoint
@russHyde
feat: dendrogram statistic ranges are centred on zero
4c3f264
@russHyde
refac: height/width of tree plot output stored in consistently-named …
a0ff2bd 
…vars in 'save_trees'
@russHyde
refac: width/height of tree-views is specified in treeview() rather t…
193227d 
…han in (non-exported) save_trees()

This makes the function call for save_trees() more similar to
save_sina_plot(), where the width and height are specified as function
arguments.
@russHyde
chore: bump version number
64ede8e
@russHyde
Merge pull request #27 from jumpingrivers/figure-formatting
7ee2741 
Figure formatting
@russHyde
add remote for {ggtree} to DESCRIPTION
ee35873
@russHyde
fix: set heatmap_offset default to old value 0.0005
8a67ec2
@russHyde
remove ggtree remote from DESCRIPTION, for bioconductor >= 3.18 the r…
cff68e4 
…emote isn't needed
@russHyde russHyde marked this pull request as ready for review October 25, 2024 19:02
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