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GiottoClass 0.4.3 (2024/11/12)
enhancements
saveGiotto()
now has include_feat_coord
param. If FALSE
, transcript coordinates will be dropped during saving, which will make the object much less memory intensive.
GiottoClass 0.4.2 (2024/10/30)
changes
makePseudoVisium()
micron_scale
(multiplicative scalefactor to get micron scaled values) supercedes micron_size
which used the inverse.
GiottoClass 0.4.1 (2024/10/28)
new
buffer()
for giottoPolygon
, giottoPoints
, spatLocsObj
. Default is to crop by voronoi borders with settleGeom()
settleGeom()
for giottoPolygon
and SpatVector
for finding non overlapping borders determined by voronoi
GiottoClass 0.4.0 (2024/10/27)
breaking changes
stop exporting deprecated internal accessors
terra requirement raised to 1.7.41 for minCircle()
bug fixes
fix dimnames()
for some subobjects
fix joinGiottoObject()
for gobjects with only poly and point data #233
fix joinGiottoObject()
for gobjects with image intensity overlaps features
fix subsetting error due to expression matrix
drop to numeric
when only one cell is left
shift_vertical_step
and shift_horizontal_step
args in createGiottoPolygonsFromMask()
when numeric now shift by steps based on the dims of the image instead of just by the numerical value provided.
fix feature metadata not being mixedsorted after join
fix non-inclusive subsetting when not all minmax values are supplied to subsetGiottoLocs()
fix giottoAffineImage
loading after being saved
enhancements
python packages to install through pip is now settable in installGiottoEnvironment()
#224
giotto
initialize()
and slot checking behavior can be toggled now using 'giotto.init'
and 'giotto.check_valid'
options. #946 by rbutleriii
setGiotto()
now only initializes and performs checks once all items are added if a list
input is provided.
instructions()
with no args will now call createGiottoInstructions()
. You can also supply named args.
instructions(gobject, param)
and instructions(gobject, param)<-
will now work for giottoInstructions
objects for convenience.
[
, [[
, $
, $<-
, and subset()
for giotto
see ?GiottoClass::subset_giotto
subset
for spatIDs()
and featIDs()
objName()
, spatUnit()
, featType()
generics now return NA_character_
instead of erroring when used on unsupported classes.
ext()
and ext<-()
can now be used to get and set extent of affine2d
rownames()
, colnames()
, dimnames()
for giotto
spatValues()
can get values from multiple spatial units.
createGiottoPolygonsFromMask()
now works with anything terra::rast()
can read
createGiottoLargeImage()
now works with anything terra::rast()
can read
new
sliceGiotto()
for pulling out specific spatial units and feature types as independent giotto
objects
splitGiotto()
for splitting a Giotto object into a list of Giotto objects based on a cell metadata column
as.list()
method for giotto
to dump the data as a list of subobjects
XY()
and XY<-()
for accessing and setting coordinate values of subobjects as matrix
terra convHull()
, minRect()
, minCircle()
for Giotto spatial vector classes
area()
for SpatVector
and giottoPolygon
GiottoClass 0.3.5 (2024/08/28)
bug fixes
intensity images now automatically scale to estimated highest value
giottoPolygon
plot()
default max_poly
raised to 1e6
giottoInstructions
no longer lose class when specific params are replaced
ometif_to_tif()
now checks for imagecodecs package as well
anndataToGiotto()
and giottoToAnndata
now check for anndata package as well.
fix joinGiottoObjects()
"z_stack"
join method
fix error in documentation #214 by shaojunyu
fix error in installGiottoEnvironment()
#1006 by 13954380607
GiottoClass 0.3.4 (2024/08/04)
bug fixes
hotfix anndata matrix support #216 by wwang-chcn
GiottoClass 0.3.3 (2024/07/29)
bug fixes
fix flipping issue with giottoAffineImage
for certain affine transforms
enhancements
missing
method for affine()
instantiates an affine2d
object
GiottoClass 0.3.2 (2024/07/26)
breaking changes
python environment installation and how it relates to default settings such as .condarc may have changed.
giottoImage
name
slot now requires character
and will not accept NULL
bug fixes
loadGiotto()
no longer errors with similarly named spat_units or feat_types (e.g. “cell” and “new_cell” would previously throw an error)
fix in giottoToSpatialExperiment()
fix for giottoToSeuratV5
for cosmx mini dataset #989 by guillermoturiel
fix issue with prints in createGiottoCosMxObject()
#960 by GBeattie
new
affine()
for giottoPolygon
, giottoPoints
, spatLocsObj
, giotto
shear()
for giottoPoints
, giottoPolygon
, spatLocsObj
, affine2d
affine2d
class for accumulating linear transforms to be used with affine()
initialize()
, [
, $
, show()
, plot()
, methods for affine2d
spin()
, rescale
, spatShift()
, affine()
, flip()
, shear()
t()
methods for affine2d
giottoAffineImage
class for just-in-time affine transformed images
initialize()
, method for giottoLargeImage
initialize()
, ext()
, crop()
, rescale()
, spatShift()
, plot()
, methods for giottoAffineImage
rescale()
method for giottoImage
spin()
, shear()
, affine()
, flip()
, t()
methods for giottoAffineImage
and giottoLargeImage
(which converts to giottoAffineImage
)
as()
conversion from giottoLargeImage
to giottoAffineImage
.get_centroid_xy()
internal for getting numeric centroid xy values of any object that responds to ext()
.bound_poly()
internal for generating a dummy polygon from the extent of any object that responds to ext()
.aff_shift_2d()
, .aff_shift_2d<-()
, .aff_linear_2d
, .aff_linear_2d()<-
internals for accessing and manipulating affine matrices
GiottoClass 0.3.1 (2024/05/21)
bug fixes
allow passing of additional params with setGiotto()
with ...
spatShift()
can now perform z shifts when start spatLocsObj
has no z information
fix bug in joinGiottoObjects()
after v0.3.0 where it looks for the now non-existent @largeImages
slot
fix bug in .update_image_slot()
after v0.3.0 where a NULL @largeImages
slot will result in an error
fix bugs in spatShift()
and rescale()
methods for giotto
when setting a default spat_unit
and feat_type
enhancements
joinGiottoObjects()
extent detection and xshift defaults now depend on ext()
of the gobject instead of any images (when available)
joinGiottoObjects()
now has a dry_run
param for previewing where datasets will be spatially located after the join
GiottoClass 0.3.0 (2024/05/13)
bug fixes
fix plot()
params passing for giottoPolygon
when type = "centroid"
fix ext()
output for giottoImage
spatShift()
and rescale()
now also affect gobject attached images #945 by rbutleriii
new
new spatValues()
to get specific values from a giotto
object in data.table
format
new ometif_to_tif
to convert between .ome.tif and .tif
new terra::density()
and terra::hist()
wrappers for giottoLargeImage
GiottoClass 0.2.3 (2024/03/12)
bug fixes
fix saveGiotto
with overwrite = TRUE
#870 by rbutlerii
fix plot()
method param passing for giottoLargeImage
. Ensure access to terra params
enhancements
createGiottoPoints
data.frame
method can now select which columns to use with x_colname
, y_colname
, feat_ID_colname
params
giotto
now responds to spatial manipulation generics: t()
, flip()
, rescale()
, spatShift()
, spin()
spatUnit()
and featType()
are now vectorized
internal get_spatial_locations_list()
and get_spatial_network_list()
accessors now accept “:all:” token to get all available, ignoring spat_unit
GiottoClass 0.2.2 (2024/03/01)
enhancements
createGiottoPolygonsFromMask()
now has ID_fmt
param for finer control of automatic poly_ID
generation
.flip_spatvect()
internal for flipping SpatVector
across arbitrary x and y vals
GiottoClass 0.2.1 (2024/02/28)
breaking changes
giotto
slot versions
supercedes OS_platform
. Used for tracking GiottoClass version.
bug fixes
fix subsetGiotto
unused on
argument
fix giotto
object saving when image intensities overlaps data are present.
fix exprObj
show()
for small matrices
fix giotto
calculateOverlap()
method when working with image intensities data.
new
createNetwork()
hub function for creation of Giotto NN and spatial networks directly from matrices. Mainly for developers and advanced users.
edge_distances()
for calculating euclidean distances from numeric m x n matrix
(nodes) and a data.table
with from and to cols that define node connections.
GiottoClass 0.1.3 (2024/01/12)
new
init_gobject
param in loadGiotto()
to control whether object initialization is also performed after load
vignette for image tools
GiottoClass 0.1.2 (2024/01/02)
Added
Added: max_window
and colors
slots to giottoLargeImage
. Use GiottoClass:::.update_giotto_image()
to update outdated objects.
Added: .bitdepth()
internal function to detect image bitdepth from sampled values
Added: re-export getMonochromeColors()
from GiottoUtils
Added: giottoPolygon
, giottoLargeImage
method for calculateOverlap()
Added: vignette for working with spatial classes
Added: output
param to .spatraster_sample_values()
. Can now return as sampled data.frame
, array
, magick
, EBImage
GiottoClass 0.1.1 (2023/12/16)
Breaking Changes
Removed: getRainbowColors()
to GiottoUtils
Removed: get_prev_fname()
and get_args()
to GiottoUtils
Removed: aggregateStacksPolygonsOLD()
Added
Added: .gstop()
for GiottoClass specific errors
Added: plot()
method for dimObj
Added: ncol()
and nrow()
methods for dimObj
Added: dimObj
additional info now accessible using $
and $<-
Added: spatEnrObj
cols now accessible using $
and $<-
Added: evaluate_input()
as exported wrapper for evaluate
functions
Added: as.polygons()
data.frame
method for correctly formatted data.tables (replaces internal dt_to_spatvector_polygon()
)
Added: as.polygons()
data.frame
method for correctly formatted data.tables (replaces internal dt_to_spatvector_points()
)
Added: autocompletes for $
with spatLocsObj
, spatEnrObj
, dimObj
, cellMetaObj
, featMetaObj
, giottoPolygon
, giottoPoints
Added: toplevel_params
param to subsetGiottoLocs()
Added: spin
, spatShift
, rescale
methods for data.frame
Changes
Fixed: Provenance now not accidentally created as a list in addSpatialCentroidLocations()
Changed: giottoPolygon
plot()
now automatically switches to centroid plotting with more than 1e4 polys
Changed: Package internal functions now have .
prefix
GiottoClass 0.1.0 (2023/11/29)
Added
Added: terraVectData
as virtual parent class for giottoPolygon
and giottoPoints
classes
Added: $
and $<-
methods for terraVectData
Added: ext<-()
method for giottoPolygon
, giottoPoints
Added: crop()
method for giottoLargeImage
, giottoPoints
Added: [
subsetting for giottoPoints
and giottoPolygon
with numerical, logical, and character (by ID)
Added: as.sf()
and as.stars()
converters for giottoPoints
and giottoPolygon
Added: setGiotto()
generic
Added: gap
param to tessellate()
which introduces a variable gap between the polygons tessellated
Added: triGrid()
Added: orthoGrid()
Added: DelayedMatrixStats to suggests
Added: calculateOverlap()
and overlapToMatrix()
as generic functions for feature and image overlap aggregations
Changes
Improved: performance of gefToGiotto()
Updated: spatIDs()
and featIDs()
methods for giottoPolygon
and giottoPoints
to allow returning non-unique IDs
Added: check for plot()
when giottoPolygon
or giottoPoints
objects contain no geometries
Added: warning for crop()
when giottoLargeImage
, giottoPolygon
, giottoPoints
objects are being cropped with an extent that does not include any information
Changed: Conversion of createGiottoPoints()
to a generic function
Deprecate: radius
param in favor of shape_size
for tessellate()
Fixed: python .install_github_link_pip()
param
Fixed: python create_AnnData()
added to globals.R