Function reference • SpatialMap

SpatialMap

SpatialMap-package: SpatialMap: Spatial biology API and exploratory analysis

createRegionObject(): User interface for the creation and validation of a new Region class object

createSpatialMap(): Create a SpatialMap object manually

Load example data

Functions that easily load example SpatialMap objects

load_sm_data() load_sm_tonsil() load_sm_skin() load_sm_data_descriptions(): Load SpatialMap's example datasets

Getters

Accessor functions to retrieve data from SpatialMap objects and Regions

projectMetadata() featureInfo() features() cells() getID() channelInfo() bgData() bgFeatures(): Methods to extract slots from SpatialMap, Region, and Analysis objects

Analyses(): List the Analysis object names in a SpatialMap

Data(): Extract data from a SpatialMap or Region objects

Regions(): List the Region object names present in a SpatialMap

Representations(): Representation

getActiveAnalysis(): Extract activeAnalysis from a SpatialMap object

getActiveRegions(): getActiveRegions

getAnalysis(): Get Analysis object from SpatialMap

getCellInteractions(): Title Export data.frame of all interactions from SpatialMap object Includes cell type notation. Output is a data.frame with rows as interactions and columns as metadata Works with FRNN, in addition to other SpatialMap NN formats.

getRegion(): Get Region object from SpatialMap

getRegionData(): Get data slot from Region object

getRegions(): Get Region objects (plural) from SpatialMap

getSMData(): Get SM Data

get_cells_in_window(): Get cells in XY window

get_channel(): Get the imaging channel number from a feature in CODEX data

get_channel.Region(): Get channel from Region

get_cycle(): Get the imaging cycle number from a feature in CODEX data

get_cycle.Region(): get_channel

get_image(): Get (greyscale) images for a Region

get_valid_metadata_counts(): Get SpatialMap metadata frequency table

get_zoom_levels(): Get zoom levels for a Region

`settings<-`() settings(): Display or set SpatialMap settings

activeAnalysis() `activeAnalysis<-`(): activeAnalysis

activeRegions(): activeRegions

Setters

Functions to safely update data in objects

`projectMetadata<-`() `featureInfo<-`() `features<-`() `cells<-`() `channelInfo<-`() `bgData<-`() `bgFeatures<-`(): Methods to set data slots for SpatialMap, Region, or Analysis objects

`settings<-`() settings(): Display or set SpatialMap settings

`Representations<-`(): Set Representations

Plotting

Plotting and visualization functions

plotCellProportions(): Plot Cell Proportions

plotChordDiagram(): plotChordDiagram Plot chord diagrams based on pairwise adjacency results.

plotCohortChordDiagram(): Grouped chord diagrams

plotCohortsVolcano(): compareCohorts volcano plot

plotExpressionHeatmap(): Plot Expression Heatmap

plotFilterSummary(): Plot CODEX filtering summaries

plotFilteredCells() plotFilteredCells.SpatialMap() plotFilteredCells.Region(): Plot Filtered Cells in Spatial Context, or by Other Representations

plotImage(): Plot Image from SpatialMap Objects

plotImage.Region(): Plot raw image annotation layer

plotImage.acquisition_id(): Plot raw image annotation layer without passing a SpatialMap region

plotModelComponents.Region(): Plot the results of the two-component mixture model

plotNeighborhoodCellCounts(): Plot Feature Counts by Neighborhood

plotPairwiseAdjacency(): Plot pairwise adjacency scores

plotPairwiseAdjacency.Region(): plotPairwiseAdjacency.Region

plotQCSummary(): plotQCSummary

plotRepresentation(): Plot Representations of Spatial Biology Data

plotViolins(): Violin Expression Plots

plotViolins.Region(): Plot Expression Violin Plots, Region

plot_chord_diagram(): plot_chord_diagram Helper function to plot a circlize circos chord diagram

neighborhoodHeatmap(): Create heatmap of cell neighborhoods

Graphs

Functions to work with graph (NN) objects

computeNearestNeighbors(): Compute Nearest Neighbor Graphs

computeNearestNeighbors.Region(): computeNearestNeighbors.Region

spatialNearestNeighbors(): Spatial cellular network graph

spatialNearestNeighbors.Region(): spatialNearestNeighbors.Region

listNNs() nn.igraph() nn.name() nn.idx() nn.dist() nn.method() nn.misc(): Methods to extract data slots from NN objects

NN-class NN: The NN class

`NN<-`(): Set a single NN

NN_to_igraph(): NN to igraph

NNs(): Retrieve graphs from an object.

`NNs<-`(): Set NNs

createFixedRadiusNNGraph.Region(): Create Fixed-Radius Nearest Neighbor (frNN) Graph

createKNNGraph.Region(): Create K Nearest Neighbor (KNN) Graph

createNN(): Create Nearest Neighbor Object

createSharedNNGraph.Region(): Create shared nearest neighbors graph

show(<NN>): Show information about NN objects

updateNNData(): Update NN Object Data

nn.GetAdjacencyMatrix(): Get an adjacency matrix from an NN object

nn.IsSymmetric(): Test if a graph is symmetric

nn.ListToMatrix(): Convert NN adjacency matrices to lists

nn.MatrixToAdjacencyList(): Convert NN adjacency matrices to lists

nn.applyDistanceCutoff(): Apply distance cutoff to NN object

nn_matrices_to_igraph(): NN matrices to igraph

createDelaunayTriangulation.Region(): Create a Delaunay triangulation

dropSelfInteractions() addSelfInteractions(): Add or Drop self-interactions from an NN object

checkSelfInteractions(): Check if self-interactions are present in the NN graph object

count_pairwise_interactions(): Count pairwise interactions

getCellInteractions(): Title Export data.frame of all interactions from SpatialMap object Includes cell type notation. Output is a data.frame with rows as interactions and columns as metadata Works with FRNN, in addition to other SpatialMap NN formats.

Common classes

SpatialMap classes that exist in this package

Analysis-class Analysis: The Analysis class

NN-class NN: The NN class

Region-class Region: The Region Class

Representation-class Representation: The Representation class

SpatialMap-class SpatialMap: The SpatialMap Class

Creators

Functions that help create from scratch or import external data

createAnalysis(): Create SpatialMap Analysis

createDelaunayTriangulation.Region(): Create a Delaunay triangulation

createFixedRadiusNNGraph.Region(): Create Fixed-Radius Nearest Neighbor (frNN) Graph

createKNNGraph.Region(): Create K Nearest Neighbor (KNN) Graph

createNN(): Create Nearest Neighbor Object

createRegionObject(): User interface for the creation and validation of a new Region class object

createRepresentation(): Create Representation

createSharedNNGraph.Region(): Create shared nearest neighbors graph

createSpatialMap(): Create a SpatialMap object manually

createSpatialMapSettings() showsettings(): SpatialMap Settings

Everything else

FilterCodex(): Filter CODEX cell data

Normalize(): Normalize Spatial Proteomics Data

QCMetrics(): QC Metrics

Repair(): Repair older SpatialMap objects

`Representations<-`(): Set Representations

SummarizeFilters(): SummarizeFilters

Trim(): Trim values

activeAnalysis() `activeAnalysis<-`(): activeAnalysis

activeRegions(<SpatialMap>): activeRegions method

`activeRegions<-`(<SpatialMap>): activeRegions-set method

`activeRegions<-`(): activeRegions-set

activeRegions(): activeRegions

addCellMetadata(): Add Cell Metadata

addFeatureInfo(): Add Feature Info

addProjectMetadata(): Add Project metadata

addRegionNames(): Add names to Regions in SpatialMap

addRepresentation(): Add a Representation to a SpatialMap or Region object

add_igraph(): Add igraph to NN

arcsinh_transform_region(): Arcsinh transform biomarker expressions with custom scale factors

autothreshold(): Auto-threshold Channel Intensity

avg_sil(): Average silhouette score

black_bg(): Add a black background to a ggplot annotation based image

calculateMutualInformation(): Compute mutual information

`$`(<Region>): $.Region

`$`(<SpatialMap>): Index into SpatialMap

cellMetadata() `cellMetadata<-`(): cellMetadata

cellNeighborhoods(): Compute cell neighborhoods

clusterCells(): Cluster cells

cluster_leiden.region(): Leiden clustering of Region data

cluster_louvain.region(): Louvain clustering of Region data

combineMaps(): Combine SpatialMap objects

compareAdjacency(): Compare the pairwise adjacency fingerprints of two cohorts of samples

compareCohorts(): Compare Cohorts

cubic_root_region(): Cube root transform biomarker expressions

custom_scale_region(): Normalize data with custom scale factors

defaultCategoricalColors(): Return a default set of categorical colors

defaultContinuousColors(): defaultContinuousColors

defaultTheme(): defaultTheme

default_color_scale(): Default color scale

differentialExpression(): Compute Differential Expression Across Groups

differential_wilcox(): Compute Wilcox test for expression differences between groups of cells

differential_wilcox.Region(): Compute Wilcox test for expression differences between groups of cells

dim(<Region>) dim(<Analysis>): Extract the dimensions (cells by features) of a Region object

.aggregated_interaction_counts(): .aggregated_interaction_counts

.create_filename_mapping(): Helper function to create a named character vector of IDs to file names.

.smapply(): SpatialMap apply over Regions

.smc(): Low-level merging of Regions

.smgroup(): SpatialMap Group Samples

.validCellMetadata(): Check if cellMetadata are valid

.validSpatialMap(): Check validity of SpatialMap object

dynamic.threshold(): Dynamically threshold

embeddings(): Retrieve embeddings

exportAnnotations(): Export annotations

exportCellData(): Export combined cell data

exportCoords(): Export coordinates

exportData(): Export expression data

exportMetadata(): Export projectMetadata

exportPathDefault(): Show the default export path for export* functions

flatness(): Compute "flatness," which is the median expression value divided by the IQR.

flexible_coordinate_subset(): Flexible subsetting of a matrix by coordinates

function_scale_region(): Scaling using a custom function

infiltrationScore() infiltrationScore.Region(): Infiltration Score Between Two Phenotypes

initializeFuture(): Initialize future processing

initializePython(): Initialize Python environment

listActiveAnalysis(): listActiveAnalysis

listActiveRegions(): listActiveRegions

localEntropy.Region() localEntropy(): Local Entropy over Network Graph

log10_x(): Nice looking log10-scaled axes using ggplot2

log10_y(): Nice looking log10-scaled axes using ggplot2

log_normalize_region(): Log transform biomarker expressions

makeAnalysisFromRegion(): Update Analysis from Region

makeSpatialMapFromFCS(): Make SpatialMap from FCS files

markers_on_channel(): Get all the markers for a specified channel

mergeProjectMetadata(): Merge Project and Cell metadata

metadata_or_db(): Retrieve data from metadata or the DB

minmax_scale_region(): Min Max Scaling

model_norm_region(): Modeling noise with Gaussian Mixture Models (GMM)

names(<Region>): Get Region cellMetadata names

names(<SpatialMap>): names-SpatialMap

`names<-`(<SpatialMap>,<character>): names-SpatialMap-character-set

neighborhoodClusters(): Cluster neighborhoods

neighborhood_kmeans_helper(): Optimize K-Means with silhouette score

null_if_na(): Helper function to sub NULL if the value contains NA

numMarkersExpressed(): Number of markers expressed

num_markers_expressed_region(): Number of markers expressed - Region

pairwiseAdjacency(): Pairwise Adjacency

pull_pairwise_adjacency_results(): Helper function used in plotPairwiseAdjacency.Region and plotChordDiagram.Region Pulls pairwise adjacency results for the Region, resolving aggregate flag, then pivots data to wide (matrix) format, where feature 1 is represented by rownames and feature 2 is represented by column names, and the values are as specified by values_from

qc_metrics(): qc_metrics

rawsettings(): Raw settings

removeCellMetadata(): Remove cell metadata

robust_scale_region(): Outlier-robust data scaling

runPCA(): Run PCA

runPCA.Region(): Run PCA

runUMAP(): Run UMAP

runUMAP.Region(): Run UMAP on Region-type objects

sameSM(): Test if two SpatialMap objects are identical

setRegionID(): Set Region ID

`settings<-`() settings(): Display or set SpatialMap settings

show(<Analysis>): Show Analysis object

show(<Region>): Show Region object

show(<Representation>): Show Representation object

show(<SpatialMap>): Show SpatialMap object

show-SpatialMap-methods: Show methods

smSubset() .smsubset(): Subset SpatialMap

smVersion(): Check loaded SpatialMap version

spatialQC(): Heuristic Spatial Quality Control

spatialmap_from_db(): spatialmap_from_db

spatialmap_from_emobject(): Convert emObject to SpatialMap

`[[`(<Region>,<ANY>,<missing>): [[.Region

`[[`(<SpatialMap>,<ANY>,<missing>): [[.SpatialMap

subRegion(): Subset a Region object by coordinates

`[`(<Region>,<ANY>,<missing>,<ANY>) `[`(<Region>,<ANY>,<ANY>,<ANY>) `[`(<Region>,<missing>,<missing>,<ANY>): Subset a Region object

`[`(<SpatialMap>,<ANY>,<missing>,<missing>): Subset a SpatialMap object

total_norm_region(): Total signal normalization

updateProjectMetadata(): Update projectMetadata

updateRegionData(): Update Region Data

uploadCellMetadata(): Upload SpatialMap metadata to the Enable Portal

uploadQC(): Upload QC results to Portal

version(): Check SpatialMap version

which_analysis(): Determine how .smapply dispatches functions

which_returns(): Parse output from .smapply iterator

z_scale_region(): z_scale_region