Merge pull request #815 from drieslab/suite_dev

v3.3.2

.gitignore

@@ -9,3 +9,4 @@ merfish_preoptic/
 .vscode/*
 .Rprofile
 inst/python/.ipynb_checkpoints/
+docs

DESCRIPTION

@@ -109,6 +109,7 @@ Suggests:
     smfishHmrf,
     SPARK,
     SpatialExperiment,
+    spdep,
     SummarizedExperiment,
     tiff,
     trendsceek,
@@ -143,6 +144,7 @@ Collate:
     'interactivity.R'
     'interoperability.R'
     'poly_influence.R'
+    'python_bento.R'
     'python_environment.R'
     'python_hmrf.R'
     'python_scrublet.R'
@@ -154,6 +156,7 @@ Collate:
     'spatial_interaction_visuals.R'
     'spatial_structures.R'
     'spatial_visuals.R'
+    'spdep.R'
     'utilities.R'
     'utils-pipe.R'
     'variable_genes.R'

NAMESPACE

@@ -50,6 +50,8 @@ export(calculateOverlapParallel)
 export(calculateOverlapPolygonImages)
 export(calculateOverlapRaster)
 export(calculateOverlapSerial)
+export(calculateSpatCellMetadataProportions)
+export(callSpdep)
 export(cellProximityBarplot)
 export(cellProximityEnrichment)
 export(cellProximityEnrichmentEachSpot)
@@ -85,6 +87,7 @@ export(comparePolygonExpression)
 export(convertEnsemblToGeneSymbol)
 export(convertGiottoLargeImageToMG)
 export(createArchRProj)
+export(createBentoAdata)
 export(createCellMetaObj)
 export(createCrossSection)
 export(createDimObj)
@@ -141,13 +144,15 @@ export(dimPlot2D)
 export(dimPlot3D)
 export(distGiottoImage)
 export(doCellSegmentation)
+export(doClusterProjection)
 export(doFeatureSetEnrichment)
 export(doGiottoClustree)
 export(doHMRF)
 export(doHMRF_V2)
 export(doHclust)
 export(doKmeans)
 export(doLeidenCluster)
+export(doLeidenClusterIgraph)
 export(doLeidenSubCluster)
 export(doLouvainCluster)
 export(doLouvainSubCluster)
@@ -229,7 +234,8 @@ export(giottoMasterToSuite)
 export(giottoPoints)
 export(giottoPolygon)
 export(giottoToAnnData)
-export(giottoToSeurat)
+export(giottoToSeuratV4)
+export(giottoToSeuratV5)
 export(giottoToSpatialExperiment)
 export(heatmSpatialCorFeats)
 export(heatmSpatialCorGenes)
@@ -332,11 +338,14 @@ export(runIntegratedUMAP)
 export(runPAGEEnrich)
 export(runPAGEEnrich_OLD)
 export(runPCA)
+export(runPCAprojection)
+export(runPCAprojectionBatch)
 export(runPatternSimulation)
 export(runRankEnrich)
 export(runSpatialDeconv)
 export(runSpatialEnrich)
 export(runUMAP)
+export(runUMAPprojection)
 export(runWNN)
 export(runtSNE)
 export(saveGiotto)
@@ -364,8 +373,8 @@ export(set_spatialGrid)
 export(set_spatialNetwork)
 export(set_spatial_enrichment)
 export(set_spatial_locations)
-export(seuratToGiotto)
-export(seuratToGiotto_OLD)
+export(seuratToGiottoV4)
+export(seuratToGiottoV5)
 export(showCellProportionSwitchedPie)
 export(showCellProportionSwitchedSanKey)
 export(showClusterDendrogram)
@@ -437,6 +446,7 @@ export(spatialAutoCorGlobal)
 export(spatialAutoCorLocal)
 export(spatialDE)
 export(spatialExperimentToGiotto)
+export(spdepAutoCorr)
 export(specificCellCellcommunicationScores)
 export(stitchFieldCoordinates)
 export(stitchGiottoLargeImage)

NEWS.md

@@ -1,4 +1,21 @@
 
+# Giotto Suite 3.3.2 (Release TBD)
+
+## Breaking Changes
+
+## Added
+- Added `checkPythonPackage()` within `python_environment.R` to check for a python package within a provided environment, and install that package there if it is not found. Supports github url installation. Supports package version specification, but not version minima, maxima, or ranges (i.e., "pysodb==1.0.0" is supported, "pysodb>=1.0.0" is not)
+- Added `py_install_prompt()` within `python_environment.R` to prompt a user to install a python package within a provided environment
+- Added `install_github_link_pip()` within `python_environment.R` to use pip to install a python package from a github link within a provided environment after prompting the user.
+- Added `install_py_pkg_reticulate()` within `python_environment.R` to install a specified python package  within a provided environment via `reticulate::py_install()` after prompting the user.
+- New file `python_bento.R`
+- Added `createBentoAdata()` within `python_bento.R` to create a bento-flavor anndata object from a Giotto Object
+
+## Changes
+- Improved performance of gefToGiotto()
+- Added `env_name` as an argument to `anndataToGiotto()` and `giottoToAnnData()` for compatability with `checkPythonPackage()`
+- Deprecated internal function `check_py_for_scanpy()` in favor of new function `checkPythonPackage()`
+
 
 # Giotto Suite 3.3.1 (2023-08-02)
 
@@ -28,10 +45,10 @@
 ## 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()` with `plot_last` parameter. Default output now plots polygons above points for better visibility.
+- Updated `polyStamp()` to replace an apply function with a crossjoin for better performance
+- Updated `spatInSituPlotPoints()` with `plot_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. 
+- 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
@@ -154,7 +171,7 @@
 - Fix `loadGiotto()` loss of over-allocation for data.tables-based objects after loading from disk
 
 
-# Giotto Suite 3.1.0 (2202-12-01)  
+# Giotto Suite 3.1.0 (2022-12-01)  
 
 
 ## Added
@@ -209,7 +226,7 @@
 
 
 
-# Giotto Suite 2.1.0 (2202-11-09)
+# Giotto Suite 2.1.0 (2022-11-09)
 
 ## Breaking Changes
 - Update of python version to **3.10.2** [details](https://giottosuite.readthedocs.io/en/latest/additionalinformation.html#giotto-suite-2-1-0-2202-11-09)

R/auxiliary_giotto.R

@@ -4774,6 +4774,146 @@ calculateMetaTableCells = function(gobject,
 
 
 
+#' @title calculateSpatCellMetadataProportions
+#' @name calculateSpatCellMetadataProportions
+#' @description calculates a proportion table for a cell metadata column (e.g. cluster labels)
+#' for all the spatial neighbors of a source cell. In other words it calculates the
+#' niche composition for a given annotation for each cell.
+#' @param gobject giotto object
+#' @param spat_unit spatial unit
+#' @param feat_type feature type
+#' @param spat_network spatial network
+#' @param metadata_column metadata column to use
+#' @param name descriptve name for the calculated proportions
+#' @param metadata_cols annotation columns found in \code{pDataDT(gobject)}
+#' @param return_gobject return giotto object
+#' @return giotto object (default) or enrichment object if return_gobject = FALSE
+#' @export
+calculateSpatCellMetadataProportions = function(gobject,
+                                                spat_unit = NULL,
+                                                feat_type = NULL,
+                                                spat_network = NULL,
+                                                metadata_column = NULL,
+                                                name = 'proportion',
+                                                return_gobject = TRUE){
+
+
+  if(is.null(spat_network)) stop('spat_network = NULL, you need to provide an existing spatial network')
+  if(is.null(metadata_column)) stop('metadata_column = NULL, you need to provide an existing cell metadata column')
+
+  # Set feat_type and spat_unit
+  spat_unit = set_default_spat_unit(gobject = gobject,
+                                    spat_unit = spat_unit)
+  feat_type = set_default_feat_type(gobject = gobject,
+                                    spat_unit = spat_unit,
+                                    feat_type = feat_type)
+
+  # get spatial network to use
+  sp_network = get_spatialNetwork(gobject = gobject,
+                                  spat_unit = spat_unit,
+                                  name = spat_network,
+                                  output = 'networkDT')
+
+  # convert spatial network to a full spatial network
+  sp_network = convert_to_full_spatial_network(reduced_spatial_network_DT = sp_network)
+
+  # get cell metadata
+  cell_meta = get_cell_metadata(gobject = gobject,
+                                spat_unit = spat_unit,
+                                feat_type = feat_type,
+                                output = 'data.table')
+
+  # merge spatial network and cell metadata
+  network_annot = data.table::merge.data.table(network, cell_meta[,c('cell_ID', metadata_column), with = FALSE], by.x = 'source', by.y = 'cell_ID')
+  setnames(network_annot, old = metadata_column, 'source_clus')
+  network_annot = data.table::merge.data.table(network_annot, cell_meta[,c('cell_ID', metadata_column), with = FALSE], by.x = 'target', by.y = 'cell_ID')
+  setnames(network_annot, old = metadata_column, 'target_clus')
+
+  # create self information: source cell is its own neighbor
+  source_annot_info = unique(network_annot[,.(source, source_clus)])
+  setnames(source_annot_info, 'source_clus', 'label')
+  source_annot_info[, target := source]
+  source_annot_info = source_annot_info[,.(source, target, label)]
+
+  # network information: source cells and other neighbors
+  target_annot_info = unique(network_annot[,.(source, target, target_clus)])
+  setnames(target_annot_info, 'target_clus', 'label')
+
+  # combine: provides most detailed information about neighbors
+  final_annot_info = rbindlist(list(source_annot_info, target_annot_info))
+
+
+
+  # calculate proportions of neighbors
+  tableres = final_annot_info[, names(table(label)), by = 'source']
+  setnames(tableres, 'V1', 'tablelabels')
+  propensities = final_annot_info[, prop.table(table(label)), by = 'source']
+  setnames(propensities, 'V1', 'proptable')
+
+
+  # data.table variables
+  label = NULL
+  propensities[, label := tableres$tablelabels]
+  propensities[, proptable := as.numeric(proptable)]
+  proportions_mat = dcast.data.table(propensities, formula = 'source~label', fill = 0, value.var = 'proptable')
+  data.table::setnames(x = proportions_mat, old = 'source', new = 'cell_ID')
+
+  # convert to matrix
+  # proportions_matrix = dt_to_matrix(proportions_mat)
+  # proportions_matrix[1:4, 1:10]
+
+  # create spatial enrichment object
+  enrObj = create_spat_enr_obj(name = name,
+                               method = 'rank',
+                               enrichDT = proportions_mat,
+                               spat_unit = spat_unit,
+                               feat_type = feat_type,
+                               provenance = NULL,
+                               misc = NULL)
+
+
+  ## return object or results ##
+  if(return_gobject == TRUE) {
+
+    spenr_names = list_spatial_enrichments_names(gobject = gobject,
+                                                 spat_unit = spat_unit,
+                                                 feat_type = feat_type)
+
+
+    if(name %in% spenr_names) {
+      cat('\n ', name, ' has already been used, will be overwritten \n')
+    }
+
+    ## update parameters used ##
+    parameters_list = gobject@parameters
+    number_of_rounds = length(parameters_list)
+    update_name = paste0(number_of_rounds,'_spatial_enrichment')
+
+
+    ## update parameters used ##
+    gobject = update_giotto_params(gobject, description = '_enrichment')
+
+    ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+    gobject = set_spatial_enrichment(gobject = gobject,
+                                     spatenrichment = enrObj)
+    ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+    return(gobject)
+
+  } else {
+
+    return(enrObj)
+
+  }
+
+
+
+}
+
+
+
+
+
 #' @title combineMetadata
 #' @name combineMetadata
 #' @description This function combines the cell metadata with spatial locations and