Releases: drieslab/Giotto
Releases · drieslab/Giotto
v4.0.0
v3.3.2
v3.3.1
Breaking Changes
- Change
checkGiottoEnvironment()
. Downgrade from error to message and return FALSE when a provided directory does not exist
Added
- New file
poly_influence.R
- New function
showPolygonSizeInfluence()
withinpoly_influence.R
to show if cells switch clusters when across resized polygon annotations - New function
showCellProportionSwitchedPie()
withinpoly_influence.R
to visualize results fromshowPolygonSizeInfluence()
in a pie chart - New function
showCellProportionSwitchedSankey()
withinpoly_influence.R
to visualize results fromshowPolygonSizeInfluence()
in a Sankey diagram - New function
makePseudoVisium()
withingiotto_structure.R
to generate a pseudo visium grid of circular spots - New function
tessellate()
withingiotto_structure.R
to generate a grid of hexagons or squares for spatial binning - New file
feature_set_enrichment.R
- New function
doFeatureSetEnrichment()
withinfeature_set_enrichment.R
for GSEA analysis - New function
doGiottoClustree()
withinclustering.R
for visualizations of leiden clusters at varying resolutions - New
createArchRProj()
andCreateGiottoObjectFromArchR()
functions to create agiotto
object with ATAC or epigenetic features using the ArchR pipeline. - New
giottoMasterToSuite()
function to convert agiotto
object created with the master version to a Giotto suite object. - New
readPolygonVizgenParquet()
for updated parquet outputs - Add checkmate to Imports for assertions checking
- Add exported
create
function forexprObj
creation - New file
spatial_manipulation.R
- Add
ext()
methods forgiottoPolygon
,giottoPoints
,spatialNetworkObj
,spatLocsObj
,giottoLargeImage
- Add
flip()
methods forgiottoPolygon
,giottoPoints
,spatialNetworkObj
,spatLocsObj
,SpatExtent
,giottoLargeImage
- Add access to terra plotting params for
giottoLargeImage
plot()
method.
Changes
- Fix bug in
combine_matrices()
- Fix bug in
createGiottoObject()
that will not allow object creation without supplied expression information - Updated
polyStamp()
to replace an apply function with a crossjoin for better performance. - Updated
spatInSituPlotPoints()
withplot_last
parameter. Default output now plots polygons above points for better visibility. - Add check for spatLocsObj for spatlocs in polyStamp()
- Removed various print() and cat() statements throughout.
- Changed default verbose argument to FALSE for createGiottoObject
- Changed default verbose argument to FALSE for joinGiottoObjects
- Changed default verbose argument to FALSE for createGiottoObjectSubcellular
- Default verbose = FALSE argument added to cellProximityEnrichmentSpots
- Default verbose = FALSE argument added to specific_CCCScores_spots
- Default verbose = FALSE argument added to runWNN
- Default verbose = FALSE argument added to subset_giotto_points_object
- Default verbose = FALSE argument added to subset_feature_info_data
- Default verbose = FALSE argument added to subsetGiotto
- Default verbose = FALSE argument added to subsetGiottoLocsSubcellular
- Default verbose = FALSE argument added to createGiottoXeniumObject_subcellular
- Update
readPolygonFilesVizgenHDF5()
add option to return asdata.table
and skipgiottoPolygon
creation. DownstreamgiottoPolygon
creation refactored as new internal function - Update cell segmentation workflow to check for deepcell and PIL python packages
- Update cell segmentation workflow to return grayscale mask images instead of RGB
- Update
createGiottoVisiumObject()
image h5 scalefactors reading to use partial matching for whether hi or lowres image is supplied - Update
giottoLargeImage
plot()
method to useterra::plot()
instead ofterra::plotRGB()
for grayscale images - Remove unnecessary prints from
subsetGiotto()
- Fix bug in
readCellMetadata()
andreadFeatMetadata()
v3.3.0
Breaking Changes
- Removed all deprecated accessors from
accessors.R
set_default_feat_type()
error downgraded to warning when nofeat_type
s exist for givenspat_unit
- update
loadGiotto()
andsaveGiotto()
to allow using long strings as column names in the spatVector objects 'active_spat_unit'
and'active_feat_type'
params that can be set throughinstructions()
are now used instead of 'giotto.spat_unit' and 'giotto.feat_type' global options- removed duplicate
create_dimObject()
internal function. Keepingcreate_dim_obj()
Added
- New implementations of
anndataToGiotto()
andgiottoToAnnData()
for Nearest Neighbor and Spatial Networks - New
check_py_for_scanpy()
function, shifting code around inanndataToGiotto()
- Add
initialize()
method forgiotto
- Add exported
create
constructor functions for Giotto S4 subobjects - Add
activeSpatUnit()
andactiveFeatType()
for getting and setting active defaults on gobject - New
get_*_list()
internal functions for retrieving list of all objects of a particular class for a spat_unit and feat_type - Add
instructions()
generic forgiotto
to access and editgiottoInstructions
- Add
centroids()
method forgiottoPolygon
to get centroid info - Add
overlaps()
generic for accessingoverlaps
slot ofgiottoPolygon
- Add
[
and[<-
(empty) access generics to get the data from main slots ofgiottoPolygon
andgiottoPoints
- Add cores detection to run on package attach. (
getOption('giotto.cores')
) - Add option to return as
giottoPoints
fromgetFeatureInfo
(default is stillSpatVector
) - Add
spatVector_to_dt2
internal as a barebones alternative tospatVector_to_dt()
- Add
getRainbowColors()
color palette - New
assign_objnames_2_list()
andassign_listnames_2_obj()
internals for passing list names to object@name
slots and vice versa - New test_that
test_createObject.R
script forread
functions/S4 subobject creation - New test_that
test_accessors.R
script foraccessor
functions - New test_that
test_gobject.R
script for gobject consistency checks
Changes
- Update
installGiottoEnvironment()
and downstream internal functions to allow custom python installation with a new argument,mini_install_path
. - Update
checkGiottoEnvironment()
to account for custom python installations with a new argument,mini_install_path
. - Update
removeGiottoEnvironment()
to account for custom python installations with a new argument,mini_path
. - Update
createGiottoObject()
with new data ingestion pipeline - Modify
cell_ID
,feat_ID
,cell_metadata
,feat_metadata
slot initialization - Update
read_expression_data()
andevaluate_expr_matrix()
to be compatible withexprObj
- Change
changeGiottoInstructions()
to allow addition of new params and enforce logical class of known params - Update and fix bugs in
createGiottoCosMxObject()
associated with polygon placement and generation - Update
plot()
forgiottoPoints
with faster rasterized plotting option. (Now used by default) - Fix bug in
doLouvainCluster()
(sub)functions and made them compatible with new Giotto Suite framework. - Fix bug in
gefToGiotto()
bin_size arguments. - Update
loadGiotto()
andsaveGiotto()
with path.expand to expand provided file/directory paths - Organize new and refactored slot
check
functions ingiotto.R
for checking gobject consistency duringinitialize()
- Organize new and refactored
evaluate
functions indata_evaluation.R
for data wrangling of external data - Organize new and refactored
read
functions indata_input.R
for ingesting data and converting to list of Giotto native S4 subobjects - Organize dummy documentation in
dd.R
for inheriting commonly used documentation - Moved
create_featureNetwork_object()
,create_giotto_points_object()
,create_giotto_polygon_object()
to classes.R - Moved
depth()
from giotto.R to utilities.R
v3.2.0
(Originally Released 2023-02-02)
Breaking Changes
- Removed support for deprecated nesting in
@nn_network
slot createSpatialNetwork()
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
- Only
createGiottoCosMxObject()
subcellular
workflow available until the others are updated
Added
- New
gefToGiotto()
interoperability function to convert gef object from Stereo-seq to giotto - New
giottoToAnnData()
interoperability function to convert giotto object to squidpy flavor anndata .h5ad file(s) - New
giottoToSpatialExperiment()
andspatialExperimentToGiotto()
to convert between Giotto and SpatialExperiment - New
spatialAutoCorLocal()
andspatialAutoCorGlobal()
functions to find spatial autocorrelations from expression and cell metadata information - New
createSpatialWeightMatrix()
function to generate spatial weight matrix from spatial networks for autocorrelation - Add 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 reference - New
fread_colmatch()
internal for fread loading a subset of rows based on matches in a specified column - Add 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 flexible - Add
optional
andcustom_msg
params topackage_check()
- New
wrap()
andvect()
generics forgiotto
,giottoPoints
, andgiottoPolygons
- New
rotate()
,t()
, andspatShift
generics for giotto subobject spatial manipulation - New
spatIDs()
andfeatIDs()
generics - New
objName()
andobjName
generics for setting the names of relevant S4 subobjects - New
rbind()
generic to appendgiottoPolygon
objects - Add packages
exactextractr
andsf
to "suggests" packages - Add 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 columns - Update
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 allowed - Fix bug in
loadGiotto()
that prevents proper parsing of filenames when spat_unit or feat_type contains '_' characters - Fix
loadGiotto()
loss of over-allocation for data.tables-based objects after loading from disk
v3.0.1
v1.1.0
This is the first release after merging the development branch with master following the 'ours' strategy as detailed in https://stackoverflow.com/questions/2862590/how-to-replace-master-branch-in-git-entirely-from-another-branch
The previous master branch is copied to a new branch called 'old_master'.
v1.0.4
v1.0.3
v1.0.0
Full update on Giotto.
See https://rubd.github.io/Giotto_site/news/index.html#giotto-1-0-0 for more details.