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Seurat v3.2.1 #3479

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merged 171 commits into from
Sep 7, 2020
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808b2c9
add default assay, and slot
yuhanH Jul 17, 2020
08a41d2
Fix style
mojaveazure Jul 17, 2020
094b4df
Bump develop version
mojaveazure Jul 17, 2020
af0bee5
Run devtools::document
mojaveazure Jul 17, 2020
b068a59
Merge pull request #345 from satijalab/fix/UMAP_slot
mojaveazure Jul 17, 2020
1bb25fb
set maxized ncells and remove duplicates
yuhanH Jul 17, 2020
6dddae2
Support for FIt-SNE 1.2+
saketkc Jul 17, 2020
928576f
Style changes
saketkc Jul 18, 2020
0b10417
Merge branch 'develop' into fitsne_121
Jul 24, 2020
7e87df8
Fixes to interactive SpatialDimPlot
mojaveazure Jul 24, 2020
33df324
version 1.0 -> 1.0.0, only pass pca argument to Rtsne
andrewwbutler Jul 27, 2020
9cc79ae
update NEWS and bump develop version
andrewwbutler Jul 27, 2020
457fc84
Merge pull request #3281 from satijalab/fitsne_121
andrewwbutler Jul 27, 2020
d17ac92
Merge branch 'develop' into fix/ISpatialDimPlot
andrewwbutler Jul 28, 2020
e67c4e0
update NEWS and bump develop version
andrewwbutler Jul 28, 2020
32822ae
Merge pull request #351 from satijalab/fix/ISpatialDimPlot
andrewwbutler Jul 28, 2020
f7e627a
minor style tweaks, add tests
andrewwbutler Jul 28, 2020
cd3db37
Merge branch 'develop' into fix/TopCells_oddcell
andrewwbutler Jul 28, 2020
b48e820
update NEWS and bump develop version
andrewwbutler Jul 28, 2020
ad0008e
Merge pull request #348 from satijalab/fix/TopCells_oddcell
andrewwbutler Jul 28, 2020
cfb992e
just return top one for num=1
andrewwbutler Jul 29, 2020
44f3702
change round to ceiling
yuhanH Jul 29, 2020
c3afd00
put round back
yuhanH Jul 29, 2020
bdff1a6
bump develop version
andrewwbutler Jul 29, 2020
7be0547
add NN input RunUMAP
yuhanH Jul 29, 2020
63a86f9
Merge pull request #354 from satijalab/fix/TopN1
andrewwbutler Jul 29, 2020
790083e
nn name in umap.seurat
yuhanH Jul 29, 2020
8f02427
add docu
yuhanH Jul 29, 2020
0d1501b
fix to logging if functions run with do.call
andrewwbutler Jul 30, 2020
2703ac1
Stacked violin plot with two way clustering
jaisonj708 Jul 31, 2020
92fe81d
updating docs
jaisonj708 Jul 31, 2020
4284cc1
fix transform
jaisonj708 Jul 31, 2020
671defd
named color vector for DoHeatmap
Jul 31, 2020
d03d78f
bump develop version and update NEWS
andrewwbutler Jul 31, 2020
a1f2f73
Merge pull request #356 from satijalab/fix/Log_docall
andrewwbutler Jul 31, 2020
96eb351
update
yuhanH Aug 3, 2020
b4e1d28
minor style tweaks
andrewwbutler Aug 3, 2020
c65aa92
Merge branch 'develop' into feat/UMAP_NN
andrewwbutler Aug 3, 2020
e5738c9
update NEWS and bump develop version
andrewwbutler Aug 3, 2020
7b5ce9b
Merge pull request #355 from satijalab/feat/UMAP_NN
andrewwbutler Aug 3, 2020
17ad2a6
Merge branch 'develop' into fix/HeatmapColors
andrewwbutler Aug 4, 2020
8dd3bae
update NEWS, bump develop version
andrewwbutler Aug 4, 2020
2fb38df
Merge pull request #359 from satijalab/fix/HeatmapColors
andrewwbutler Aug 4, 2020
953fa6f
small merge optimizations
andrewwbutler Aug 7, 2020
f0e8ed0
use emplace_back instead of push_back
andrewwbutler Aug 7, 2020
856320c
generalize RowMergeSparseMatrices to take list
andrewwbutler Aug 8, 2020
d4fba83
update header file
andrewwbutler Aug 8, 2020
e778d32
minor stylistic changes + comments
andrewwbutler Aug 9, 2020
cbb4303
update header file
andrewwbutler Aug 8, 2020
94073bd
minor fix
andrewwbutler Aug 9, 2020
0817996
Bump develop version
mojaveazure Aug 10, 2020
db6d027
Merge branch 'develop' into feat/MergeOptimizations
mojaveazure Aug 10, 2020
7f4c9f5
Merge pull request #363 from satijalab/feat/MergeOptimizations
mojaveazure Aug 10, 2020
84f111b
enable box labels in DimPlot, fix nonstandard colors
andrewwbutler Aug 11, 2020
f058e11
fix to exact PCA when determining whether to weight.by.var
andrewwbutler Aug 13, 2020
5b00e74
add npcs for clarity
andrewwbutler Aug 13, 2020
c1c3674
bump develop version + update NEWS
andrewwbutler Aug 13, 2020
bae8eed
Merge pull request #367 from satijalab/fix/RunPCA_exactweights
andrewwbutler Aug 13, 2020
9fd974c
prototype Neighbor class
andrewwbutler Aug 13, 2020
e42f43e
add RenameCells.Neighbor
andrewwbutler Aug 13, 2020
a3d2734
Merge pull request #365 from satijalab/fix/BoxLabels_DimPlot
epapalexi Aug 14, 2020
48bb148
Update docs for AddModuleScore
mojaveazure Aug 14, 2020
46b7d33
More documentation updates
mojaveazure Aug 14, 2020
19acb92
bump develop version, update NEWS
andrewwbutler Aug 14, 2020
8ebc10f
Merge branch 'develop' into fix/AddModuleScoreDocs
andrewwbutler Aug 16, 2020
a4bbf5a
bump develop version
andrewwbutler Aug 16, 2020
ea186b3
Merge pull request #369 from satijalab/fix/AddModuleScoreDocs
andrewwbutler Aug 16, 2020
383bc4c
add TopNeighbors fxn
andrewwbutler Aug 16, 2020
c55643d
Merge branch 'develop' into feat/MoreViolins
mojaveazure Aug 17, 2020
f024a46
custom sorting and coloring
jaisonj708 Aug 17, 2020
bdb7a10
custom coloring + orientation
jaisonj708 Aug 17, 2020
41813d2
add infrastructure around the alg.idx slot
andrewwbutler Aug 17, 2020
d441df2
add conversion fxns between Neighbor and Graph classes
andrewwbutler Aug 17, 2020
69c5909
custom color, order, orientation
jaisonj708 Aug 18, 2020
cc99833
add tests for Neighbor class
andrewwbutler Aug 18, 2020
2c9eae3
Update style
mojaveazure Aug 18, 2020
98d9e75
Update style
mojaveazure Aug 18, 2020
0845187
Update style
mojaveazure Aug 18, 2020
bebe1dc
update DESCRIPTION + fix return style
jaisonj708 Aug 18, 2020
1e4f7bf
Merge remote-tracking branch 'origin' into feat/MoreViolins
jaisonj708 Aug 18, 2020
81d4857
add uwot version check
andrewwbutler Aug 18, 2020
ac995d8
resolve merge conflict / fix return style
jaisonj708 Aug 18, 2020
77c080f
bump develop version
andrewwbutler Aug 18, 2020
01410ba
Merge pull request #374 from satijalab/fix/uwot-version
andrewwbutler Aug 18, 2020
d318a98
swap gh actions in for azure
andrewwbutler Aug 18, 2020
8eb92bd
fix offset bug when merging list of matrices
andrewwbutler Aug 18, 2020
9473a80
add merge test
andrewwbutler Aug 19, 2020
d0cc04b
Update DESCRIPTION
epapalexi Aug 19, 2020
4e261ba
Merge pull request #376 from satijalab/fix/merge
epapalexi Aug 19, 2020
5880eba
add do.shuffle feature to DimPlot
samuel-marsh Aug 21, 2020
23eeb8c
change do.shuffle to shuffle, add seed parameter
andrewwbutler Aug 21, 2020
ebb0fae
bump develop version, update NEWS
andrewwbutler Aug 24, 2020
c94010e
Merge pull request #3408 from samuel-marsh/develop
andrewwbutler Aug 24, 2020
666a5c7
Merge pull request #375 from satijalab/feat/GH_Actions2
mojaveazure Aug 25, 2020
343daae
alternative matrix row scaling implementation with matrixStats
andrewwbutler Aug 25, 2020
9e1c097
add legend, sparsify axis labels, allow split.by color
Aug 26, 2020
3aea6d1
don't clip if scale_max is Inf
cdarby Aug 26, 2020
c3c517b
Merge branch 'develop' into feat/FastRowScale_Improved
andrewwbutler Aug 26, 2020
8233af4
bump develop version
andrewwbutler Aug 26, 2020
252bcc0
Merge pull request #379 from satijalab/feat/FastRowScale_Improved
andrewwbutler Aug 26, 2020
7646420
Merge branch 'develop' into feat/NeighborClass
mojaveazure Aug 27, 2020
5125bd7
Bump develop version
mojaveazure Aug 27, 2020
84f3206
Merge pull request #368 from satijalab/feat/NeighborClass
mojaveazure Aug 27, 2020
8c6a4ff
allow Neighbor objects with only subset of cells in object
andrewwbutler Aug 27, 2020
40d1f11
Adjust grammar
mojaveazure Aug 28, 2020
ff14c36
bump develop version
andrewwbutler Aug 28, 2020
95fc472
Merge pull request #380 from satijalab/fix/NeighborFixes
andrewwbutler Aug 28, 2020
a3b6b55
Replace dashes with periods in plot data for CellSelctor
mojaveazure Aug 28, 2020
b12118c
Deprecate CreateGeneActivityMatrix
timoast Aug 28, 2020
8d53952
Add note to changelog
mojaveazure Aug 28, 2020
f8194b1
Merge pull request #383 from satijalab/feat/deprecate_gene_activity
mojaveazure Aug 28, 2020
08f7127
Raise error if not due to missing features; #3402
timoast Aug 28, 2020
beabe95
Merge branch 'develop' into fix/CellSelctorDashes
mojaveazure Aug 28, 2020
a84b549
Bump develop version
mojaveazure Aug 28, 2020
22239a2
Merge pull request #382 from satijalab/fix/CellSelctorDashes
mojaveazure Aug 28, 2020
82414c3
Merge branch 'develop' into fix/subsetassay
mojaveazure Aug 28, 2020
feee068
Update changelog
mojaveazure Aug 28, 2020
590bedf
Merge pull request #384 from satijalab/fix/subsetassay
mojaveazure Aug 29, 2020
67b114d
speed up SelectIntegrationFeatures
Aug 31, 2020
ae0e630
fix lapply call
Aug 31, 2020
358f34c
bump develop version
andrewwbutler Aug 31, 2020
845a484
Merge pull request #386 from satijalab/feat/SelectIntgFeatures
andrewwbutler Aug 31, 2020
8a59fde
update DESCRIPTION and NEWS for 3.2.1 release
andrewwbutler Aug 31, 2020
deee5d3
Deprecate ReadAlevin and ReadAlevinCsv
mojaveazure Sep 2, 2020
4c3ddda
Deprecate H5AD functionality
mojaveazure Sep 2, 2020
443b91c
Deprecate loom functionality
mojaveazure Sep 2, 2020
213e6ca
Update NEWS.md
mojaveazure Sep 2, 2020
cc2e7f8
Merge pull request #392 from satijalab/feat/deprecate_alevin
mojaveazure Sep 2, 2020
8a2ffcf
Merge branch 'develop' into feat/deprecate_disk
mojaveazure Sep 2, 2020
6d57ca7
Deprecate cell browser functionality
mojaveazure Sep 2, 2020
971af48
Move ape to suggests
mojaveazure Sep 2, 2020
d599798
Merge pull request #393 from satijalab/feat/deprecate_disk
mojaveazure Sep 2, 2020
8c74801
Merge branch 'develop' into feat/deprecate_cellbrowser
mojaveazure Sep 2, 2020
9d44e76
Merge branch 'develop' into release/3.2.1
mojaveazure Sep 2, 2020
589fba0
Merge pull request #394 from satijalab/feat/deprecate_cellbrowser
mojaveazure Sep 2, 2020
6e0b659
Update R/tree.R
mojaveazure Sep 2, 2020
b87d0a1
Merge branch 'develop' into feat/SuggestApe
mojaveazure Sep 2, 2020
8fa092d
Merge pull request #395 from satijalab/feat/SuggestApe
mojaveazure Sep 3, 2020
460789c
Merge branch 'develop' into release/3.2.1
mojaveazure Sep 3, 2020
f787a70
updating spatial labeling code, require ggplot2>=3.3.0
andrewwbutler Sep 3, 2020
95d2e51
move Indices calls outside loops
cdarby Sep 3, 2020
5eb6938
Merge pull request #398 from satijalab/fix/IndicesLoop
andrewwbutler Sep 3, 2020
e332474
Merge branch 'develop' into release/3.2.1
andrewwbutler Sep 3, 2020
653315e
Merge branch 'develop' into fix/SpatialLabels
mojaveazure Sep 3, 2020
38bbead
Update NEWS
mojaveazure Sep 3, 2020
17caa21
Merge branch 'fix/SpatialLabels' of github.com:satijalab/seurat-priva…
mojaveazure Sep 3, 2020
89023ca
Bump develop version
mojaveazure Sep 3, 2020
6d05790
Merge pull request #396 from satijalab/fix/SpatialLabels
mojaveazure Sep 3, 2020
076861a
Merge branch 'develop' into release/3.2.1
mojaveazure Sep 3, 2020
401982e
Bump minimum R version
mojaveazure Sep 4, 2020
d9ec1ee
fix ncol parameter in VizDimLoadings
andrewwbutler Sep 4, 2020
3469d5e
Fix issue where 'features' was being used prior to definition
mojaveazure Sep 4, 2020
f491970
dims not features
andrewwbutler Sep 4, 2020
37f3e5e
merge
andrewwbutler Sep 4, 2020
cd8a9a5
Update documentation for FindNeighbors
mojaveazure Sep 4, 2020
dc68faf
Merge pull request #399 from satijalab/fix/VizDimLoadingsCols
mojaveazure Sep 4, 2020
b57a149
Merge branch 'develop' into release/3.2.1
mojaveazure Sep 4, 2020
682180f
Merge branch 'develop' into feat/MoreViolins
mojaveazure Sep 4, 2020
89459b8
Update changelog
mojaveazure Sep 4, 2020
47d8f56
Merge pull request #357 from satijalab/feat/MoreViolins
mojaveazure Sep 4, 2020
1833f95
Merge branch 'develop' into release/3.2.1
mojaveazure Sep 4, 2020
9e62358
Update URLs for CRAN
mojaveazure Sep 4, 2020
69d326a
devtools::document updated these
mojaveazure Sep 4, 2020
86a817a
Merge branch 'release/3.2.1' of github.com:satijalab/seurat-private i…
mojaveazure Sep 4, 2020
c680e35
Update CRAN comments
mojaveazure Sep 4, 2020
c2f5ae1
Update README.md
mojaveazure Sep 4, 2020
36b533c
Merge branch 'develop' into fix/FindNeighborsDocs
mojaveazure Sep 4, 2020
5869ef4
Merge pull request #401 from satijalab/fix/FindNeighborsDocs
mojaveazure Sep 4, 2020
31de785
Merge branch 'develop' into release/3.2.1
mojaveazure Sep 4, 2020
932f426
Merge pull request #387 from satijalab/release/3.2.1
mojaveazure Sep 4, 2020
86d33bf
Update URLs
mojaveazure Sep 4, 2020
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change round to ceiling
  • Loading branch information
yuhanH committed Jul 29, 2020
commit 44f3702fd5a74423d97e621932c8f3b90273d48d
5 changes: 1 addition & 4 deletions R/objects.R
Original file line number Diff line number Diff line change
Expand Up @@ -8017,11 +8017,8 @@ Top <- function(data, num, balanced) {
nr, "). Setting to ", nr , ".", call. = FALSE)
num <- nr
}
if (num == 1) {
balanced <- FALSE
}
top <- if (balanced) {
num <- round(x = num / 2)
num <- ceiling(x = num / 2)
data <- data[order(data, decreasing = TRUE), , drop = FALSE]
positive <- head(x = rownames(x = data), n = num)
negative <- rev(x = tail(x = rownames(x = data), n = num))
Expand Down