Giotto Suite 3.2.0 (2023-02-02)#
Breaking Changes#
Removed support for deprecated nesting in
@nn_network
slotcreateSpatialNetwork()
will now output aspatialNetworkObj
by default whenreturn_gobject = FALSE
. It is possible to change this back to the data.table output by settingoutput = 'data.table'
Set incomplete classes in classes.R as virtual to prevent their instantiation
Removed
createGiottoCosMxObject()
aggregate
andall
workflows until they are updated
Added#
New
gefToGiotto()
interoperability function to convert gef object from Stereo-seq to giottoNew
giottoToAnnData()
interoperability function to convert giotto object to squidpy flavor anndata .h5ad file(s)New
giottoToSpatialExperiment()
andspatialExperimentToGiotto()
to convert between Giotto and SpatialExperimentNew
spatialAutoCorLocal()
andspatialAutoCorGlobal()
functions to find spatial autocorrelations from expression and cell metadata informationNew
createSpatialWeightMatrix()
function to generate spatial weight matrix from spatial networks for autocorrelationAdd spatial_interaction_spot.R with functions adapted from master branch for working with the Giotto suite object.
New exported accessors for slots (experimental)
New
multiomics
slot ingiotto
Add
coord_fix_ratio
param tospatFeatPlot2D()
andspatFeatPlot2D_single()
Add
order
parameter todimFeatPlot2D
andspatDimFeatPlot2d
to plot and order cells according to the levels of the selected feature (#477)Add
plot()
method forspatialNetworkObj
New
set_row_order_dt()
internal for settingdata.table
to a specific row order by referenceNew
fread_colmatch()
internal for fread loading a subset of rows based on matches in a specified columnAdd missing
create_nn_net_obj()
internal constructor function for S4nnNetObj
Add
id_col
,x_col
,y_col
params topolyStamp()
to make stamp location input more flexibleAdd
optional
andcustom_msg
params topackage_check()
New
wrap()
andvect()
generics forgiotto
,giottoPoints
, andgiottoPolygons
New
rotate()
,t()
, andspatShift
generics for giotto subobject spatial manipulationNew
spatIDs()
andfeatIDs()
genericsNew
objName()
andobjName
generics for setting the names of relevant S4 subobjectsNew
rbind()
generic to appendgiottoPolygon
objectsAdd packages
exactextractr
andsf
to “suggests” packagesAdd package
progressr
to “imports” packages
Changes#
Move giotto object method-specific creation functions from
giotto.R
toconvenience.R
Update
addFeatMetadata()
to handle replacement of existing columnsUpdate
show()
method forgiotto
Update
show()
method forspatEnrObj
Deprecate older snake_case accessors
Deprecate
polygon_feat_names
param in favor ofz_indices
inreadPolygonFilesVizgenHDF5()
Deprecate
xy_translate_spatial_locations()
in favor ofshift_spatial_locations()
Optimize
readPolygonFilesVizgen()
Fix bug in
replaceGiottoInstructions()
where instructions with more slots than previous are not allowedFix bug in
loadGiotto()
that prevents proper parsing of filenames when spat_unit or feat_type contains ’_’ charactersFix
loadGiotto()
loss of over-allocation for data.tables-based objects after loading from disk
Giotto Suite 3.1.0 (2202-12-01)#
Added#
New
initialize()
generic that callssetalloccol()
for data.table-based S4 subobjects to allow setting by referenceNew
spatUnit
,spatUnit<-
,featType
, andfeatType<-
feat type generics for S4 subobjects for setting the relevant slotsAdd
hexVertices()
to polygon shape array generation functionality
Changes#
Update
createGiottoCosMxObject()
for 3.0 and modularization of functions. ‘subcellular’ workflow has been tested to work along with an updated tutorial.Update grid plotting behavior to set a default number columns to use based on number of elements to plot. Can be overridden by explicitly providing input to
cow_n_col
paramFix bug in
annotateGiotto()
after 3.0 update (#433)Fix bug in
joinGiottoObjects()
metadata processingUpdate seed setting behavior in dimension_reduction.R and clustering.R
Giotto Suite 3.0.1 (2022-11-20)#
Added#
New system color support detection (based on crayon package logic)
Add ability to turn off colored text in
show
functions withoptions("giotto.color_show" = FALSE)
Changes#
Fix bug in
extract_polygon_list()
(#433)Update Unicode character printing with
show
functions for Latin1 systems
Giotto Suite 3.0.0 (2022-11-18)#
Breaking Changes#
S4 subobjects framework will require giotto objects to be remade
Added#
New
createGiottoXeniumObject()
for loading 10x Xenium dataNew S4 subobjects. Details can be found in classes.R
New basic generics for S4 subobjects. Mainly the use of
[]
and[]<-
to get or set information into the main data slotNew
@provenance
slot in S4 subobjects to track provenance of aggregated information (z_layers used for example)New
calculateOverlapPolygonImages()
for calculating overlapped intensities from image-based information (e.g. IMC, IF, MIBI, …) and polygon data (e.g. cell)New
overlapImagesToMatrix()
converts intensity-polygon overlap info into an expression matrix (e.g. cell by protein)New
aggregateStacks()
set of functions work with multiple subcellular layers when generating aggregated expression matrices
Changes#
Update
setter
functions to read the@spat_unit
and@feat_type
slots of subobjects to determine nestingUpdate of
show
functions to display color coded nesting names and tree structure
Giotto Suite 2.1.0 (2202-11-09)#
Breaking Changes#
Update of python version to 3.10.2 details
Added#
New
anndataToGiotto()
to convert scanpy anndata to Giotto
Giotto Suite 2.0.0.998#
Added#
New
GiottoData
package to work with spatial datasets associated with GiottoStores the minidatasets: preprocessed giotto objects that are ready to be used in any function
Moved:
getSpatialDataset()
andloadGiottoMini()
functions to this package
New
saveGiotto()
andloadGiotto()
for preserving memory-pointer based objects. In general_help.RIt saves a Giotto object into a folder using a specific structure. Essentially a wrapper around
saveRDS()
that also works with spatVector and spatRaster pointers.
New
plotInteractivePolygon()
for plot-interactive polygonal selection of points.New polygon shape array creation through
polyStamp()
,circleVertices
,rectVertices
. In giotto_structures.RAdd accessor functions
get_CellMetadata
(alias ofpDataDT()
),set_CellMetadata
,get_FeatMetadata
(alias offDataDT()
),set_FeatMetadata
. See accessors.RNew
filterDistributions()
to generate histogram plots from expression statistics
Changes#
Deprecate
plotInteractionChangedGenes()
,plotICG()
,plotCPG()
in favor ofplotInteractionChangedFeatures()
andplotICF()
andplotCPF()
Deprecate
plotCellProximityGenes()
, in favor ofplotCellProximityFeatures()
Deprecate
plotCombineInteractionChangedGenes()
,plotCombineICG()
,plotCombineCPG()
in favor ofplotCombineInteractionChangedFeatures()
andplotCombineICF()
Deprecate
findInteractionChangedGenes()
,findICG()
,findCPG()
in favor offindInteractionChangedFeats()
andfindICF
Deprecate
filterInteractionChangedGenes()
,filterICG()
,filterCPG()
in favor offilterInteractionChangedFeats()
andfilterICF()
Deprecate
combineInteractionChangedGenes()
,combineICG()
,combineCPG()
in favor ofcombineInteractionChangedFeats()
andcombineICF()
Deprecate
combineCellProximityGenes_per_interaction()
in favor ofcombineCellProximityFeatures_per_interaction()
Breaking Changes#
ICF output internal object structure names have changed to use feats instead of genes