High-Performance Open-Source Archive
DefaultDimReduc<- to enable users
to specify a default dimensional reduction for object interaction and
visualization (#268)assay in
FetchData.Seurat (#278).CropVisiumV2 (#279, #289)[ to specify that ordering of
cells/features is not always preserved (#280)drop = FALSE in
LayerData<-.StdAssay to preserve dimensions when setting
layer to the requested cells (#269)droplevels.meta.data to
subset.Seurat to allow users to drop unused factor levels
in object-level metadata when subsetting (#286)subset.Seurat (#265)FilterObjects in
[[<- (#275)subset.Seurat to no longer call
droplevels on the input’s cell-level meta.data
slot; update subset.Assay to no longer call
droplevels on the input’s feature-level
meta.features slot; update subset.StdAssay to
no longer call droplevels on the input’s feature-level
meta.data slot (reverting #251, see discussion in
#247)drop = FALSE when retrieving data in
LayerData.Assay to preserve dimensions when subsetting to
the requested cells (#261)sf.data slot in the Segmentation
class to store a data.frame in accordance with changes in
loading Visium segmentations (#267)compact slot to the Segmentation class
to denote whether the object only stores segmentation information in the
sf.data slot, or also the sp-inherited slots
(#267)CreateSegmentation,
CreateSegmentation.data.frame,
CreateSegmentation.sf, and methods interacting with
Segmentation objects (Cells.Segmentation,
RenameCells.Segmentation, Crop.Segmentation,
subset.Segmentation, [[<-,
coordinates, Overlay, show,
setValidity) to account for the addition of
compact and the update to sf.data
coords_x_orientation slot to the FOV
class to hold the orientation of the x-axis for spatial data (to mark
whether the coordinate system of a spatial object has been updated)UpdateSeuratObject to check whether an object
requires an update to the coordinate system based on the existence and
value of the coords_x_orientation slot (currently only
relevant for Visium objects)safeValidityCheck to show an improved error
message suggesting to run UpdateSeuratObject when a “slots
in class definition but not in object” error is thrown by R’s internal
object validation; use in FOV-interacting methodssf.data slot to the Segmentation class
to store an sf
object (#258)
sf.data will represent segmentation boundaries for a
given image inside the images slot of a Seurat objectCreateSegmentation.sf, [[<-,
setValidity for interacting with Segmentation
objectsRenameCells.Segmentation,
subset.Segmentation, [,
UpdateSeuratObjectmisc slot to SpatialImage to
store additional info associated with an object in a list (#258)subset.Seurat to call droplevels on
the input’s cell-level meta.data slot; update
subset.Assay to call droplevels on the input’s
feature-level meta.features slot; update
subset.StdAssay to call droplevels on the
input’s feature-level meta.data slot (#251)UpdateSeuratObject to call
droplevels on the input’s cell-level meta.data
slot (@samuel-marsh, #247)Seurat from Enhances; update
.IsFutureSeurat to avoid calling
requireNamespace('Seurat', ...) (#250)VariableFeatures.StdAssay setter to apply a
speedup (#240)SVFInfo.Assay5 &
SpatiallyVariableFeatures.Assay5 (#242)UpdateSeuratObject (@neanderthalensis, #210)WhichCells.Seurat (@maxim-h, #219)SpatiallyVariableFeatures.Assay (#242)merge.Seurat (#246)VariableFeatures.StdAssay (#245)HVFInfo.StdAssay (#244)RenameCells.Seurat (#237)subset.StdAssay (#214)%||% from rlang (#178)UpdateSeuratObject (@ddiez, #182)... to call signature for Radius
generic (#190)PolyVtx (#194)UpdateSeuratObject to run without
Seurat installed (#199)Layers.Assay() when the search returns
no results (@maxim-h,
#189)subset to allow empty images to be dropped
(#204)GetAssayData() to use
layer instead of slot (#160)SaveSeuratRds() to move all
layers instead of just those in tempdir() (#169)SetAssayData() to use
layer instead of slot (#171)FilterObjects() to
.FilterObjects() (#171)Assay5 class with support for layers; layers
provide support for:
$ method for Assay and
Assay5 objects to pull expression matrices, replacing
informal usage of @LayerData() and LayerData()<-
functions to replace GetAssayData() and
SetAssayData(), respectivelydimnames()<- (changing feature names does not apply to
v3 Assay objects)SaveSeuratRds() and LoadSeuratRds() to
save and load Seurat objects with disk-backed layersdroplevels.LogMap() to drop unused entries from a
LogMapsplit()) and rejoin layers
(JoinLayers()) within Assay and
Assay5 objects based on grouping factorslot argument deprecated in all contexts; where
applicable, replaced with layer argument[ for Assay and Assay5
objects take a layer name to pull an expression matrix
Seurat.object.assay.brackets allows restoring
v3/v4 behavior of subsetting the main expression matrix (eg.
data)PackageCheck() deprecated in favor of
rlang::check_installed()AttachDeps() deprecated in favor of using the
Depends field of DESCRIPTIONSeurat object may have subsets of
cells present at the object levelstop() and warning()
with rlang::abort() and rlang::warn() for
easier debuggingKeyMixin
objectsAssay(),
Seurat())CellsByIdentities (#80)Assays and DimReducs in
UpdateSeuratObject when missingUpdateSeuratObject to work when data
is NULL (#38)FOV, Segmentations,
Centroids, and Molecules classes for
imaging-based spatial datasetsCreateSeuratObject.Assay sets Assay key when not
present (#29)Assay from a data
frame (#32)CheckMatrix generic for validating expression
matricesKey.Seurat (#26)Seurat.checkdots option if
option is not set (#16)head and tail methods for
Seurat and Assay objects (#5)AttachDeps to attach required imported dependencies on
package attachmentIsMatrixEmpty to test if a matrix is empty or notAssay objects to replace
Seurat::SCTAssay or Signac::ChromatinAssay
objects of the same namedata.table/tibble objects (#4)NULL if a subset results in zero
cells (#9)
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