Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Refactoring package #1

Merged
merged 105 commits into from
Oct 13, 2023
Merged
Changes from 1 commit
Commits
Show all changes
105 commits
Select commit Hold shift + click to select a range
ee88e80
Update workflow triggers
TheOafidian Jul 31, 2023
950bfde
Change name to tidytacos
TheOafidian Jul 31, 2023
d3c5685
Change logo
TheOafidian Jul 31, 2023
5143276
Update links
TheOafidian Jul 31, 2023
91d2fc2
Remove deprecated functions
TheOafidian Jul 31, 2023
39a801b
Remove add_alphas synonym from example
TheOafidian Jul 31, 2023
b2a8476
Remove deprecated functions from function descriptions
TheOafidian Aug 1, 2023
11c5710
Update README and DESCRIPTION
SWittouck Aug 1, 2023
9c93678
Merge branch 'dev' of github.com:lebeerlab/tidytacos into dev
SWittouck Aug 1, 2023
261bd0e
Update pkgdown style
TheOafidian Aug 1, 2023
99f3f5e
Merge branch 'dev' of github.com:LebeerLab/tidytacos into dev
TheOafidian Aug 1, 2023
580f8ff
Add Sarah to authors
SWittouck Aug 1, 2023
b4c1b53
Merge branch 'dev' of github.com:LebeerLab/tidytacos into dev
TheOafidian Aug 1, 2023
9e057d7
Remove references to synonyms
TheOafidian Aug 1, 2023
f31a2d1
Remove synonym
TheOafidian Aug 1, 2023
09e89f1
Renaming to tidytacos
TheOafidian Aug 1, 2023
871c0cf
User input validation for bar_plot
TheOafidian Aug 1, 2023
e538d29
Merge remote-tracking branch 'origin/master' into dev
TheOafidian Aug 1, 2023
32bd67c
List taxa per user distinct condition
TheOafidian Aug 1, 2023
ab42f56
Simple ggvendiagram plot to show overlapping asvs
TheOafidian Aug 1, 2023
690a829
Add tests
TheOafidian Aug 2, 2023
b90445a
Add function to make sure optional dependency is loaded
TheOafidian Aug 2, 2023
0f67bf3
Plotly as optional dep
TheOafidian Aug 2, 2023
d70e762
Fix quosure bug in pcoa_plot_ly
TheOafidian Aug 2, 2023
127d140
Finish feature
SWittouck Aug 2, 2023
e461561
Merge branch 'feature/shared-asvs' into dev
SWittouck Aug 2, 2023
66b5d29
Documentation updates
TheOafidian Aug 2, 2023
07a7478
Merge branch 'dev' of github.com:LebeerLab/tidytacos into dev
TheOafidian Aug 2, 2023
b9865eb
Alter taxonlist function in test
TheOafidian Aug 2, 2023
77dbfb6
Update urt dataset to new format
TheOafidian Aug 2, 2023
3446a97
Remove some redundant functions
SWittouck Aug 2, 2023
63188a9
Use tacoplot_ prefix
TheOafidian Aug 2, 2023
6a6b13c
Merge branch 'dev' of github.com:lebeerlab/tidytacos into dev
SWittouck Aug 2, 2023
0aabb33
Merge branch 'dev' of github.com:lebeerlab/tidytacos into dev
SWittouck Aug 2, 2023
f2c1ff2
Remove non-functional vdiffr tests for plotly plots
TheOafidian Aug 2, 2023
a115fa9
Make some functions internal
SWittouck Aug 2, 2023
63e3bfe
Merge branch 'dev' of github.com:LebeerLab/tidytacos into dev
TheOafidian Aug 3, 2023
21e68e0
Adapt tests to changes urt testdata
TheOafidian Aug 3, 2023
c935f4e
Remove alias function call
TheOafidian Aug 3, 2023
9395397
Renamed abundances table to counts, renamed abundance variable to rea…
TheOafidian Aug 3, 2023
d397f27
Add non-interactive pcoa plot
TheOafidian Aug 7, 2023
b646fde
Rename plotting func
TheOafidian Aug 9, 2023
58a72a5
Change error to warning, so operations on label can be performed
TheOafidian Aug 29, 2023
41d0657
Skip tests for optional dependencies if they're not installed
TheOafidian Sep 9, 2023
cc0e375
Install optional dependencies in gh actions
TheOafidian Sep 9, 2023
248ae4c
Don't test against development version R
TheOafidian Sep 9, 2023
8f03821
Merge branch 'dev' into rename-abundance
TheOafidian Sep 9, 2023
6c5ce19
Fix typo in count(s)
TheOafidian Sep 9, 2023
02ece76
Rename to count
TheOafidian Sep 11, 2023
ddf9d16
Merge pull request #4 from LebeerLab/rename-abundance
TheOafidian Sep 11, 2023
e22a10c
Rename add_lib_sizes to add_total_counts
TheOafidian Sep 11, 2023
55236e7
Add CLR handler
TheOafidian Sep 11, 2023
bf3eba1
Adapt to new total_counts name
TheOafidian Sep 11, 2023
8e83d4e
Add compositions package to suggests
TheOafidian Sep 11, 2023
04a0026
Add unittest for add_spike_ratio
TheOafidian Sep 11, 2023
672a2a8
Merge branch 'dev' into feature/clr
TheOafidian Sep 11, 2023
0b022d9
Initial function declaration
Sep 11, 2023
0404c1b
Merge branch 'dev' into feature/absolute-abundance
TheOafidian Sep 11, 2023
a7d83af
Add columnames to define qties
TheOafidian Sep 11, 2023
6b7a5b2
Unpack quosures and add warning if spike not found
TheOafidian Sep 11, 2023
a2df759
Merge pull request #5 from LebeerLab/feature/clr
TheOafidian Sep 12, 2023
35fbb20
Expanded absolute abundances based on spike
Sep 12, 2023
74d89f9
Rewrite matrix operations
TheOafidian Sep 12, 2023
e02dc85
Initial functions
TheOafidian Sep 12, 2023
f902ab5
Add some docstrings
TheOafidian Sep 12, 2023
66a0263
Add clr transform test
TheOafidian Sep 14, 2023
947c567
Merge branch 'dev' into feature/sparcc
TheOafidian Sep 14, 2023
41e4ba8
Add small tests for network funcs
TheOafidian Sep 14, 2023
f9e3e52
Sort output clr test
TheOafidian Sep 14, 2023
1fdb593
Update snapshot
TheOafidian Sep 15, 2023
1d6e4d4
Merge branch 'dev' into feature/sparcc
TheOafidian Sep 15, 2023
25a92f1
Replace clr test with total sum of all counts and small tolerance
TheOafidian Sep 15, 2023
7adfc50
Replace clr test with total sum of all counts and small tolerance
TheOafidian Sep 15, 2023
0e2fb69
Update codecov badge
TheOafidian Sep 15, 2023
9ba5364
Check test coverage on dev
TheOafidian Sep 15, 2023
2f00336
Add optional dependencies to coverage test
TheOafidian Sep 15, 2023
140f08f
Update documentation/namespace
TheOafidian Sep 18, 2023
b9867ef
Add absolute abundance & density tests
TheOafidian Sep 18, 2023
47d8e97
Merge pull request #8 from LebeerLab/feature/absolute-abundance
TheOafidian Sep 18, 2023
49c2ae9
Fix bug in example
TheOafidian Sep 18, 2023
84d52d9
Convert tiyamplicons to tidytacos on the fly
TheOafidian Sep 18, 2023
9cefc68
Merge branch 'dev' into feature/sparcc
TheOafidian Sep 18, 2023
1353f21
Add ord in a modular way
TheOafidian Sep 18, 2023
6a69120
Add optional dependencies
TheOafidian Sep 18, 2023
6c14551
Update docstring
TheOafidian Sep 19, 2023
47254e1
Add binary option for distance calculation
TheOafidian Sep 21, 2023
027539a
Merge pull request #9 from LebeerLab/feature/different-ords
TheOafidian Sep 21, 2023
fd6e231
Homogenize network function names
TheOafidian Sep 21, 2023
d121f05
Adapt tests to namechange
TheOafidian Sep 21, 2023
0505389
Overwrite ord data with warning if it is already present
TheOafidian Sep 21, 2023
65d64e6
Allow clustering of a single taxon if asked for
TheOafidian Sep 21, 2023
a889642
Remove excessive filter
TheOafidian Sep 21, 2023
0887af1
Plot more colors with tacoplot_stack
TheOafidian Sep 22, 2023
ddbb1dc
Changed "residual" to "other taxa"
Sep 25, 2023
e7c5f2a
Merge branch 'dev' of github.com:LebeerLab/tidytacos into dev
Sep 25, 2023
907cbd2
Fix typo
TheOafidian Sep 25, 2023
993e77a
Merge branch 'dev' of github.com:LebeerLab/tidytacos into dev
Sep 25, 2023
45dba76
Add from_dada function
TheOafidian Sep 25, 2023
e5fa100
Merge remote-tracking branch 'origin/dev' into dev
TheOafidian Sep 25, 2023
0c9d106
Rename add_total_count downstream
TheOafidian Sep 25, 2023
98acca5
Pass sample_name to sparcc
TheOafidian Sep 26, 2023
bb351be
Use palette supplied by function in tacoplot_ord_ly
TheOafidian Sep 26, 2023
5918800
Join scaled pca values by sample lable
TheOafidian Sep 26, 2023
c411206
Join eigentaxa on user supplied sample column
TheOafidian Sep 26, 2023
533488b
Fix user supplied sample names
TheOafidian Sep 26, 2023
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Fix typo
  • Loading branch information
TheOafidian authored Sep 25, 2023
commit 907cbd28096c9c6b25e203f5457ab900c7f9d5fb
2 changes: 1 addition & 1 deletion R/plotters.R
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ tacoplot_stack <- function(ta, n = 12, x = sample_clustered, geom_bar = T) {
# Add > 12 colors if asked for
if (n > 12) {
force_optional_dependency("RColorBrewer")
supressMessages(
suppressMessages(
plot <- plot +
scale_fill_manual(values = colorRampPalette(palette_xgfs)(n)))
}
Expand Down