Staging wp5 #19

russHyde · 2022-12-07T10:32:00Z

Staging branch for work package 5

Changes introduced:

treeview() outputs both .rds or .html versions of interactive tree plots and sina plots by default (and can be called to just output .rds or output .html) Create html and rds treeviews by default #18
cluster mutation lookup tables for "defining" and "all" mutations are exported by treeview() as .csv Mutation lookup tables #21
create_browser_data() function added to make all figures/files required by tfpbrowser Prep browser data #24

Save sina-plot .rds files

…clusters

Mutation lookup tables

…ve plots

Create html and rds treeviews by default

Prep browser data

russHyde and others added 24 commits December 6, 2022 15:50

env: bump roxygen version

1ef0d7a

refac: separate creation from saving of sina-cluster plot

2073e9a

feat: save sina-plot as ggplot2 in .rds file

9f9005f

chore: bump version

953a5cf

feat: treeview() user can specify sina-plot output format (rds or html)

fb33244

feat: allow saving sina-cluster plots as both html and rds

364dcaa

Merge pull request #17 from jumpingrivers/sinaplot-rds

ba25896

Save sina-plot .rds files

refac: function to get mutation-lists from a data.frame defining the …

fca0313

…clusters

feat: create cluster-mutation lookup tables

0295c11

Merge pull request #21 from jumpingrivers/mut-lookups

da1ae81

Mutation lookup tables

refac: rename treeview() param for specifying sina-plot output format

f979d24

feat: save_trees() can output interactive trees to .rds or .html

475a98a

feat: treeview() outputs either .rds or .html (or both) for interacti…

1b065ed

…ve plots

feat: save_trees() can export html, rds or both for interactive plots

e40dc26

refac: simplify tests for filepaths created by save_trees()

8ddf13b

chore: bump version

10979d7

env: use htmlwidgets >= 1.6.0 to fix a bug with pandoc paths

e2e0545

Merge pull request #18 from jumpingrivers/optional-html-treeview

0c0daf3

Create html and rds treeviews by default

ci: remove document() pre-commit hook

0ff9e89

feat: create files required by tfpbrowser using create_browser_data()

43bce39

fix: ensure correct cluster IDs are added to node-lookup tables

f81d006

add notes on how to set up tfpbrowser files using tfpscanner

0f1bafa

Merge pull request #24 from jumpingrivers/prep-browser-data

a4f0fbc

Prep browser data

bump version

eacccf4

russHyde closed this Jul 6, 2023

russHyde reopened this Jul 6, 2023

russHyde merged commit eacccf4 into master Jul 10, 2023

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