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Release v2.1.0 #157

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Feb 23, 2024
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f16da6a
bump version and date
samuel-marsh Feb 2, 2024
4637819
multigroup clustered dotplot
samuel-marsh Feb 2, 2024
3435a52
Update docs
samuel-marsh Feb 2, 2024
da729a8
update changelog
samuel-marsh Feb 2, 2024
f717751
bump version
samuel-marsh Feb 2, 2024
f3f9c86
suppress messages
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85e836e
bump version
samuel-marsh Feb 2, 2024
83a4a14
update pkgdown yml
samuel-marsh Feb 5, 2024
7fa540d
fix error if underscore present
samuel-marsh Feb 5, 2024
eab5b75
fix underscore more
samuel-marsh Feb 5, 2024
9d664f7
fix legend
samuel-marsh Feb 5, 2024
0fe1d6e
mod plot to fit labels
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f0a7ed1
update docs
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0bd2423
fix plots
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f8fefea
fix both
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810c99f
adjustment
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76ff544
fix plot size
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98b65cf
fix width
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2f3d257
revert
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update docs
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158dcce
add ... for testing
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update docs
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2d98fd9
add padding
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57592b6
allow TRUE plot_padding and simplify
samuel-marsh Feb 7, 2024
dd8fe3b
change default padding measurements
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864fbc1
add param manual and fix warning
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c914459
Update docs
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c45b337
bump version and date
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43e6a02
fix single
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670180a
fix default padding
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b92200a
change padding defaults
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02cbedf
update vignettes
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ecab774
deprecate warnings
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2bc3351
fix deprecate lifecycle
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336e355
move deprecated separately
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2f75ea8
add deprecated
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update docs
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a49e43b
add additional deprecated functions
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85531c1
update deprecated
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572f45a
fix deprecated
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652cf46
update docs
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bump version
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d74dd94
Update deprecated
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0c23191
Update meta_present_liger
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dd68674
Meta_Present update and parameter deprecation
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147449c
update docs
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9cd234e
update changelog
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21306f9
adjust meta_present code
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b179f6d
style
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d670f62
Update docs
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ac0fb50
move to deprecated
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updatre deprecated
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update docs
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fd01946
add sce suggest
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e8e543d
mitoribo sce trial
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a6152ff
add sce method
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9d34f09
trial
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c0fed53
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remove sce
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fb32961
bump version and date
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62e3b9e
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5fe35ea
add split layers
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46cab99
add split_layers
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915de63
update namespace
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e9ef100
update docs
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b6048f4
Update changelog
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87dc4ba
bump version
samuel-marsh Feb 8, 2024
d7bac11
add multiple layer support
samuel-marsh Feb 8, 2024
5acfb9c
change from abort
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519411f
fix deprecation
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e696015
fix test code
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29bae5d
bump version
samuel-marsh Feb 8, 2024
1753b66
fix warning
samuel-marsh Feb 8, 2024
0c1cd22
move to abort
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77ae048
update verbose
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898ec1a
update split layers
samuel-marsh Feb 9, 2024
bde31d4
fix split layers
samuel-marsh Feb 9, 2024
4535a70
change warning
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4edd305
fix deprecation warnings and meta_present parameters
samuel-marsh Feb 9, 2024
7b1dcb3
deprecated
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d877f78
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5b3eb67
pkgdown test
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56ea3be
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7b05180
update release
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0350d44
fix split.by
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e1a3f6e
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8dc99d2
typo
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d9305ce
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e04cf90
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7ad6763
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e61609b
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adf4296
github actions test
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b1c5056
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samuel-marsh Feb 12, 2024
2741689
bump version and date
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ea82457
dont run
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2bdf7e4
update docs
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f19b9c4
reverting testing
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dbf5ea5
update checks to v4
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af01933
typo
samuel-marsh Feb 12, 2024
f04ef77
typo
samuel-marsh Feb 12, 2024
9586da8
dontrun
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7009f46
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f9f41f2
error two
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8a23e75
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f75d0e3
error test 3
samuel-marsh Feb 12, 2024
12d70e7
return to normal
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ce9c17c
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ba1d155
update
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f8c1b3b
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f5804b1
test method
samuel-marsh Feb 14, 2024
8cae832
namespace
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a0b06bc
seurat test
samuel-marsh Feb 14, 2024
f4d01f5
oops
samuel-marsh Feb 14, 2024
36d7302
fix
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81582c4
fix export
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d870f08
fix
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59773e8
fix
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2e68f2c
reexport
samuel-marsh Feb 14, 2024
31338bb
reexport
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31d6f7f
update conversion
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d11ef4f
update namespace
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1e0ea37
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samuel-marsh Feb 14, 2024
fb88b9d
update & add reexport
samuel-marsh Feb 15, 2024
aeb909f
update code link
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cea636c
update docs
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93087b3
Update changelog
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8424335
Update deprecated layout
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ddfa30c
Update docs
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6b84147
bump date
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59d193d
update generic manual entries
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ae50046
update docs
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c8f8f3e
update manual entries
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2ff4466
update docs
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631ab85
update manual
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19d6bf5
more manual updates
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61563df
update docs
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a98ee80
update manual examples
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1c00874
manual update
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d2a77d4
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b5d74f5
Update deprecated
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update docs
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c44b269
update vignettes
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608038f
vignette update
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0c5ebe7
fix links
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dfa8ef8
build site
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5662b83
update
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ce6d48b
update vignettes
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239346f
update date
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4cf0814
test
samuel-marsh Feb 15, 2024
a0c7524
fix
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5bf3d5a
fix link
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7120776
update docs
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967090a
site build
samuel-marsh Feb 15, 2024
4392bb3
fix feature checking
samuel-marsh Feb 15, 2024
4b85517
fix feature checking
samuel-marsh Feb 15, 2024
13e263c
feature fix
samuel-marsh Feb 15, 2024
f874fea
fix assays
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c1f5309
fix feature check
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e1764a4
typo
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4530132
Update changelog
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79a0322
update docs
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2b2ee8e
update docs
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da87565
update changelog
samuel-marsh Feb 15, 2024
e3ac0f2
Rename gene_present to feature_present and soft-deprecate gene_present
samuel-marsh Feb 15, 2024
c8a93a7
Update internal code to feature_present
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5d74c56
Update changelog
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25f2cac
update docs
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560176f
update cran comments
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4562b5a
update dates
samuel-marsh Feb 16, 2024
92ab337
extra assay check
samuel-marsh Feb 16, 2024
66ef3f6
add sct check
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05b2c9e
typo
samuel-marsh Feb 16, 2024
f270671
different title
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c51a947
add alt feature id
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a595f95
Update docs
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df9b7bc
Update changelog
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update tags
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31e79fb
update pkgdown yml
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9298bfe
update docs
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afe5663
yml edit fix
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ee6dfba
update tags
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yml update
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Update docs
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revert typo
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fix errors
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1cc6ba5
move verbose message
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bb46819
update manual
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0cf7362
update vignettes
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45be3b2
typo
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update docs
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acb936a
fix typo
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64d159c
Update changelog
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bbc41da
fix group.by dotplot
samuel-marsh Feb 21, 2024
537310f
Update changelog
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19a817f
cran submision
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change to character to prevent CRAN check error
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12e4871
cran comments
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3dc6ad7
fix cran check error
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828c4e2
fix loss of column used for dataset in meta data transfer to liger
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cran comments
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cran comments
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565c52d
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cran submit
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add dont test
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1716402
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fa7ff29
check just ggprism mod
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5700227
change dont run
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580a20b
add test
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2a35f02
update for test
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c6ef8cb
finding test issue
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3d8135d
fix
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1b93853
revert
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25e5688
test again
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385d9c9
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b607940
temp fixing
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0e876a6
revert and use PR
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406d804
temp ggprism fix?
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e25bca5
add liger version check
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d861e79
specify ggplot2 version for now until ggprism is updated
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Update cran comments
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540e745
ggplot 3.5.0 temp ggprism fix
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72c55fe
adjust liger conversion for multiple layers
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samuel-marsh committed Feb 5, 2024

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
commit 810c99f3579959b682c6598c046f23709771c3c4
12 changes: 8 additions & 4 deletions R/Plotting_Utilities.R
Original file line number Diff line number Diff line change
@@ -1283,7 +1283,8 @@ Clustered_DotPlot_Multi_Group <- function(
cluster_rows = cluster_ident,
cluster_columns = cluster_feature,
row_names_max_width = row_width,
column_names_max_height = column_height)
column_names_max_height = column_height,
heatmap_width = unit(1.5, "npc"))
} else {
cluster_dot_plot <- ComplexHeatmap::Heatmap(exp_mat,
heatmap_legend_param=list(title="Expression", labels_gp = gpar(fontsize = legend_label_size), title_gp = gpar(fontsize = legend_title_size, fontface = "bold")),
@@ -1301,7 +1302,8 @@ Clustered_DotPlot_Multi_Group <- function(
cluster_rows = cluster_feature,
cluster_columns = cluster_ident,
row_names_max_width = row_width,
column_names_max_height = column_height)
column_names_max_height = column_height,
heatmap_width = unit(1.5, "npc"))
}
} else {
if (isTRUE(x = flip)) {
@@ -1321,7 +1323,8 @@ Clustered_DotPlot_Multi_Group <- function(
cluster_rows = cluster_ident,
cluster_columns = cluster_feature,
row_names_max_width = row_width,
column_names_max_height = column_height)
column_names_max_height = column_height,
heatmap_width = unit(1.5, "npc"))
} else {
cluster_dot_plot <- ComplexHeatmap::Heatmap(exp_mat,
heatmap_legend_param=list(title="Expression", labels_gp = gpar(fontsize = legend_label_size), title_gp = gpar(fontsize = legend_title_size, fontface = "bold")),
@@ -1339,7 +1342,8 @@ Clustered_DotPlot_Multi_Group <- function(
cluster_rows = cluster_feature,
cluster_columns = cluster_ident,
row_names_max_width = row_width,
column_names_max_height = column_height)
column_names_max_height = column_height,
heatmap_width = unit(1.5, "npc"))
}
}