Package: phenoscapR 0.2.0.9001

R. Heller

phenoscapR: Read, Analyse, and Visualise Single-Cell Spatial Biology Data

Tools for importing, processing, analysing, and visualising single-cell spatial biology data from multiplexed imaging platforms. Supports cell-table quality control, marker normalisation, phenotype summaries, spatial neighbourhood statistics such as Ripley's K function (Ripley (1977) <doi:10.1111/j.2517-6161.1977.tb01615.x>) and Moran's I (Moran (1950) <doi:10.2307/2332142>), and explicit sample and coordinate-frame registries. Patient-level inference enumerates label allocations for declared contrasts (exact permutation tests; Pitman (1937) <doi:10.2307/2984124>) and retains unavailable hypotheses when adjusting for multiple testing. Grouped summaries expose missingness, eligibility, and denominator provenance. Optional canonical cell-table import uses 'cellspecR' <https://github.com/CTTIR/cellspecR>; optional Self-Organising Nebulous Growths (SONG) embeddings (Senanayake et al. (2021) <doi:10.1109/TNNLS.2020.3023941>) use 'songR' <https://github.com/CTTIR/songR>. Both optional packages are available from <https://cttir.r-universe.dev>.

Authors:R. Heller [aut, cre, cph], E. Chteinberg [aut, cph], H. Witte [aut, cph]

phenoscapR_0.2.0.9001.tar.gz
phenoscapR_0.2.0.9001.zip(r-4.7-any)phenoscapR_0.2.0.9001.zip(r-4.6-any)phenoscapR_0.2.0.9001.zip(r-4.5-any)
phenoscapR_0.2.0.9001.tgz(r-4.6-any)phenoscapR_0.2.0.9001.tgz(r-4.5-any)
phenoscapR_0.2.0.9001.tar.gz(r-4.7-any)phenoscapR_0.2.0.9001.tar.gz(r-4.6-any)
phenoscapR_0.2.0.9001.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phenoscapR/json (API)

# Install 'phenoscapR' in R:

install.packages('phenoscapR', repos = c('https://cttir.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cttir/phenoscapr/issues

Pkgdown/docs site:https://cttir.github.io

Datasets:

phenoscapR_example - Synthetic multiplexed-imaging example dataset

On CRAN:

bioinformatics data-visualization ggplot2 single-cell spatial-proteomics

5.00 score 1 stars 1 packages 11 scripts 195 exports 23 dependencies

Last updated from:72fb1bc9bc. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	404
source / vignettes	OK	406
linux-release	OK	382
macos-release	OK	299
macos-oldrel	OK	277
windows-devel	OK	359
windows-release	OK	351
windows-oldrel	OK	348
wasm-release	OK	140

Exports:AdjustPatientFamilies AlterationMatrixData AnnotateClusters AnnotationTracks ApplyGroupedThresholds as_Seurat as_SpatialCellData as_SpatialExperiment AssemblePairedSummaries AssignFixedGrid BestSubWindow BootstrapMedianInterval BoxPlot BuildExactDelaunayEdges cell_density CellDensity CellMap CellMapData CellPositionsFor CellularNeighbourhoods ClusterLabelPositions CompareArrays CompareTables CompleteRegisteredValues ComposeFigure CompositeFields CompositionPlot ContrastGroupedOverlap ContrastGroupedRanks ContrastPatientEndpoints Coords CorrelateGroupedRanks CountDisjointEdges CountRadiusSets CreateSpatialObject CrossNNDistance CustomGradient DelaunayNetwork DensestGridWindow DensityLevelContour DensityPlot DifferentialAbundance DimPlot DotPlot EmbeddingLayers EmbeddingLimits EmbeddingPlot Embeddings ExactPairedTests ExactPatientTests ExactPermutationBound ExpressionClusters FeaturePlot FieldCellsRanked FieldCentre FigureGrammars FigureGrob FigurePanel FigureText FindNeighbours FormatP FormatStatistic FormatTemplate FromCellspec GetData GetPalette HistogramPlot Idents interaction_matrix InteractionMatrix InteractionPlot LeaveOnePatientOut LegendKeys LookupNestedRows ManuscriptPalettes ManuscriptStyle MarkerHeatmap Markers Meta MoransI NCells nearest_neighbours NearestLabelDistance NearestPartnerPairs NeighbourhoodEnrichment NeighbourTypeCounts NiceBreaks NMarkers normalise_markers NormaliseData PairCorrelation PairedDifferences PaletteContinuous PaletteDiscrete PermutationCorrelation phenotype_cells PhenotypeCells PhenotypeSummary PlanExactDelaunayWorkspace plot_cell_map plot_density plot_heatmap plot_interactions PlotAlterationMatrix PlotAnnotatedHeatmap PlotBandProfiles PlotBars PlotCellMap PlotDataBindColumns PlotDataBindRows PlotDataCollapse PlotDataConstant PlotDataContrastSummary PlotDataCount PlotDataCrossShares PlotDataDirection PlotDataDominant PlotDataFromArrays PlotDataJoin PlotDataKeyColours PlotDataLabels PlotDataLonger PlotDataMembership PlotDataPairRatio PlotDataProduct PlotDataQuantiles PlotDataRankRows PlotDataRatio PlotDataRecode PlotDataRelative PlotDataSelect PlotDataShares PlotDataSummarise PlotDataTableCells PlotDataUnite PlotDensityOutlines PlotDotMatrix PlotEmbedding PlotFluorescenceField PlotGroupDifferences PlotGroupStrip PlotImage PlotIntervalForest PlotPairedPatients PlotQuantileCurves PlotScatterGroups PlotStackedBars PlotTerritories PlotTextBlock PlotVolcano ProjectSpatialTable PtLinewidth qc_filter QCFilter QCPlot QuadratAnalysis read_spatial ReadCosMx ReadFigureSpec ReadMatrixCoords ReadMERSCOPE ReadPlotTable ReadSpatial ReadXenium Reductions RenderFigure RidgePlot RipleysK run_app RunPCA RunSONG RunTSNE RunUMAP SaveFigure SchematicShapes ScreePlot SetPalette show spatial_clusters SpatialClusters SpatialDomains SpatialNetworkPlot summarise_phenotypes SummarizeCellComposition SummarizeComparisons SummarizeFixedGrid SummarizeGroupedCountFractions SummarizeGroupedValues SummarizeNearestDistances TerritoryTiles ThemeManuscript TypesetLabel VarianceExplained ViolinPlot WriteFigure

Dependencies:cli cpp11 data.table dbscan digest farver generics ggplot2 glue gtable isoband labeling lifecycle png R6 RColorBrewer Rcpp rlang S7 scales vctrs viridisLite withr

Advanced Capabilities

Rendered fromphenoscapR-05-advanced.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-06-12

Advanced Spatial Analysis

Rendered fromphenoscapR-03-spatial-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-05-04

Getting Started with phenoscapR

Rendered fromphenoscapR.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-05-04

Visualisation Gallery

Rendered fromphenoscapR-04-visualisation.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-06-12

The SpatialCellData Object

Rendered fromphenoscapR-02-object-model.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-05-04

Help page	Topics
Subset a SpatialCellData Object	[,SpatialCellData-method
Access Metadata Columns with [[	[[,SpatialCellData-method
Access Metadata Columns with $	$,SpatialCellData-method
Adjust Explicitly Declared Patient-Test Families	AdjustPatientFamilies
Alteration Classes for an Alteration Matrix	AlterationMatrixData
Annotate Clusters by Their Top Markers	AnnotateClusters
Coloured Annotation Tracks	AnnotationTracks
Apply Supplied Group Thresholds to Observations	ApplyGroupedThresholds
Convert a SpatialCellData to a Seurat Object	as_Seurat
Convert a Seurat or SpatialExperiment Object to SpatialCellData	as_SpatialCellData
Convert a SpatialCellData to a SpatialExperiment Object	as_SpatialExperiment
Assemble Registered Paired Summaries	AssemblePairedSummaries
Assign Physical Cell Coordinates to Fixed Square Grids	AssignFixedGrid
Sub-Window with the Most Cells of a Kind	BestSubWindow
Bootstrap Percentile Interval of a Median	BootstrapMedianInterval
Box Plot of Marker Expression	BoxPlot
Build Explicitly Ordered Delaunay Graphs	BuildExactDelaunayEdges
Compute Cell Density	cell_density
Cell Density (SpatialCellData)	CellDensity
Plot Cell Map	CellMap
Cells of a Map Field or Whole Section	CellMapData
Attach Cell Positions to a Table of Cell References	CellPositionsFor
Cellular Neighbourhoods (Niches)	CellularNeighbourhoods
Label Positions of Clusters on an Embedding	ClusterLabelPositions
Compare Table Columns or Arrays with Arrays of a NumPy Archive	CompareArrays
Compare a Recomputed Table with a Reference Table by Key	CompareTables
Complete Numeric Observations Against an Explicit Registry	CompleteRegisteredValues
Compose a Multi-Panel Figure	ComposeFigure
Composite Fluorescence Images from Channel Fields	CompositeFields
Stacked Bar Plot of Phenotype Composition	CompositionPlot
Contrast Explicit Groups Within Finite-Metric Overlap Strata	ContrastGroupedOverlap
Compare Two Distributions Within Explicit Groups	ContrastGroupedRanks
Exact Two-Group Contrasts for a Registry of Patient Endpoints	ContrastPatientEndpoints
Get Spatial Coordinates	Coords Coords,SpatialCellData-method
Correlate Paired Ranks Within Explicit Groups	CorrelateGroupedRanks
Count Undirected Edges Between Disjoint Node Sets	CountDisjointEdges
Count Reference Sets Within Explicit Euclidean Radii	CountRadiusSets
Create a SpatialCellData Object from Existing Data	CreateSpatialObject
Cross Nearest Neighbour Distance	CrossNNDistance
Create a Custom Gradient Palette from Anchor Colours	CustomGradient
Delaunay Triangulation Network	DelaunayNetwork
Centre of the Densest Grid Window	DensestGridWindow
Density Level Region of Each Group on an Embedding	DensityLevelContour
Plot Cell Density	DensityPlot
Differential Abundance of Phenotypes Across Conditions	DifferentialAbundance
Get Dimensions of a SpatialCellData Object	dim,SpatialCellData-method
Dot Plot of Marker Expression	DotPlot
Layered Point Data for an Embedding	EmbeddingLayers
Display Limits of an Embedding	EmbeddingLimits
Plot a Dimensionality-Reduction Embedding	DimPlot EmbeddingPlot
Get a Dimensionality-Reduction Embedding	Embeddings Embeddings,SpatialCellData-method
Exact Paired Sign-Flip Tests of Within-Subject Differences	ExactPairedTests
Exact Allocation Tests of Independent Patient Endpoints	ExactPatientTests
Lower Bound of an Exact Two-Sided Permutation P Value	ExactPermutationBound
Expression-Based Cell Clustering	ExpressionClusters
Feature Plot in Tissue Space	FeaturePlot
Cells of One Type inside a Field, Ranked	FieldCellsRanked
Field Centre as Plot Data	FieldCentre
Figure Plot Builders Available to Figure Specifications	FigureGrammars
Place a Grob on a Figure Page	FigureGrob
Describe One Figure Panel	FigurePanel
Place Text on a Figure Page	FigureText
Find Nearest Neighbours (SpatialCellData)	FindNeighbours
Format P Values for Figures	FormatP
Format a Patient-Level Statistic Line	FormatStatistic
Fill Text Templates from Table Rows	FormatTemplate
Import a Canonical Cell Table Without Losing Spatial Identity	FromCellspec
Get Expression Data	GetData GetData,SpatialCellData-method
Histogram of Marker Expression	HistogramPlot
Get Active Cell Identities	Idents Idents,SpatialCellData-method
Spatial Interaction Matrix	interaction_matrix
Interaction Matrix (SpatialCellData)	InteractionMatrix
Plot Spatial Interaction Heatmap	InteractionPlot
Exact Patient Omission Diagnostics for Declared Hypotheses	LeaveOnePatientOut
Legend Keys as a Grob	LegendKeys
Look Up Values Stored on Nested Row Subsets	LookupNestedRows
Manuscript Palettes	ManuscriptPalettes
Manuscript Figure Style	ManuscriptStyle
Plot Marker Heatmap	MarkerHeatmap
Get Marker Names	Markers Markers,SpatialCellData-method
Get or Set Cell Metadata	Meta Meta,SpatialCellData-method
Moran's I Spatial Autocorrelation	MoransI
Get the Number of Cells	NCells NCells,SpatialCellData-method
Compute Nearest Neighbour Distances	nearest_neighbours
Distance to the Nearest Cell of Given Labels	NearestLabelDistance
Cells Paired with Their Nearest Partner Cell	NearestPartnerPairs
Neighbourhood Enrichment Analysis	NeighbourhoodEnrichment
Count Neighbour Types over a Delaunay Graph with an Edge-Length Cut	NeighbourTypeCounts
Tick Breaks of Common Plotting Code	NiceBreaks
Get the Number of Markers	NMarkers NMarkers,SpatialCellData-method
Normalise Marker Intensities	normalise_markers
Normalise Marker Intensities (SpatialCellData)	NormaliseData
Pair Correlation Function	PairCorrelation
Build Paired Differences from Wide Subject Tables	PairedDifferences
Generate a Continuous Colour Palette Function	PaletteContinuous
Generate Discrete Colours	PaletteDiscrete
Permutation Test of a Rank or Linear Correlation	PermutationCorrelation
Synthetic multiplexed-imaging example dataset	phenoscapR_example
Phenotype Cells by Marker Thresholds	phenotype_cells
Phenotype Cells (SpatialCellData)	PhenotypeCells
Phenotype Summary (SpatialCellData)	PhenotypeSummary
Preflight Integer Workspace Bounds for Exact Delaunay Construction	PlanExactDelaunayWorkspace
Plot Cell Map	plot_cell_map
Plot Density Map	plot_density
Plot Marker Heatmap	plot_heatmap
Plot Interaction Heatmap	plot_interactions
Alteration Matrix	PlotAlterationMatrix
Annotated Heatmap	PlotAnnotatedHeatmap
Profiles over Ordered Categories	PlotBandProfiles
Bars per Unit	PlotBars
Cell Map	PlotCellMap
Bind Plot Data Tables	PlotDataBindColumns PlotDataBindRows
Add a Constant Column	PlotDataConstant
Summary of a Family of Two-Group Tests	PlotDataContrastSummary
Counts and Shares by Group	PlotDataCount
Shares of One Category within Another	PlotDataCrossShares
Count of Units in the Direction of an Estimate	PlotDataDirection
Order Groups by Their Dominant Category	PlotDataDominant
Table from a List of Arrays	PlotDataFromArrays
Join Columns of Another Table	PlotDataJoin
Key Colours from a Categorical Palette	PlotDataKeyColours
Text Labels from Table Rows	PlotDataCollapse PlotDataLabels
Reshape Wide Columns into Long Plot Data	PlotDataLonger
Flag Rows Whose Key Occurs in Another Table	PlotDataMembership
Ratios Between Two Levels of a Key Column	PlotDataPairRatio
Product of Columns	PlotDataProduct
Quantile Summaries of Plot Data	PlotDataQuantiles
Rank Rows by the Sum of Selected Columns	PlotDataRankRows
Ratios Between Columns	PlotDataRatio
Recode the Values of a Column	PlotDataRecode
Scale a Column to a Reference Row	PlotDataRelative
Select Rows and Columns of Plot Data	PlotDataSelect
Shares of a Total in Several Columns	PlotDataShares
Summarise Columns by Group	PlotDataSummarise
Text-Table Cells from a Per-Unit Table	PlotDataTableCells
Paste Columns into a Key Column	PlotDataUnite
Density Outlines on an Embedding	PlotDensityOutlines
Dot Matrix	PlotDotMatrix
Embedding Scatter	PlotEmbedding
Multichannel Fluorescence Field	PlotFluorescenceField
Differences Between Groups as Segments	PlotGroupDifferences
Unit Values by Group	PlotGroupStrip
Image, Image Gallery or Schematic	PlotImage
Interval Forest with Unit Values	PlotIntervalForest
Paired Patient Lines	PlotPairedPatients
Summary Curves with Quantile Bands	PlotQuantileCurves
Scatter or Dot Rows Coloured by Group	PlotScatterGroups
Stacked Bars	PlotStackedBars
Cell Territory Map	PlotTerritories
Text Block or Text Table	PlotTextBlock
Volcano Plot of Exact Group Tests	PlotVolcano
Project Spatial Tables Without Changing Column Metadata	ProjectSpatialTable
Convert Points to a 'ggplot2' Line Width	PtLinewidth
Quality Control Filter	qc_filter
Quality Control Filter (SpatialCellData)	QCFilter
QC Scatter Plot	QCPlot
Quadrat Analysis	QuadratAnalysis
Read Single-Cell Spatial Biology Data	read_spatial
Read NanoString CosMx Cell Output	ReadCosMx
Read a Figure Specification	ReadFigureSpec
Read an Expression Matrix and a Coordinate/Metadata Table	ReadMatrixCoords
Read Vizgen MERSCOPE Cell Output	ReadMERSCOPE
Read a Plot Data Table	ReadPlotTable
Read Cell Segmentation Data into a SpatialCellData Object	ReadSpatial
Read 10x Xenium Cell Output	ReadXenium
List Available Reductions	Reductions Reductions,SpatialCellData-method
Render a Figure from a Specification	RenderFigure
Ridge Plot of Marker Expression	RidgePlot
Ripley's K Function	RipleysK
Launch the phenoscapR Shiny Application	run_app
Principal Component Analysis	RunPCA
SONG Embedding	RunSONG
t-SNE Embedding	RunTSNE
UMAP Embedding	RunUMAP
Save a Composed Figure as PDF and PNG	SaveFigure
Schematic Shapes from a Specification	SchematicShapes
Scree Plot of PCA Variance	ScreePlot
Set or Get the Default Colour Palette	GetPalette SetPalette
Show a SpatialCellData Object	show,SpatialCellData-method
Spatial Cell Clustering	spatial_clusters
The SpatialCellData Class	SpatialCellData-class
Spatial Clusters (SpatialCellData)	SpatialClusters
Spatial Domains	SpatialDomains
Plot Spatial Network	SpatialNetworkPlot
Summarise Phenotype Proportions	summarise_phenotypes
Cell-Type Composition, Densities and Declared State Fractions of a Section	SummarizeCellComposition
Summarise Comparison Results into Pass/Fail Checks	SummarizeComparisons
Summarize Cell Annotations Within Fixed Grids	SummarizeFixedGrid
Summarize Grouped Subset Counts as Fractions	SummarizeGroupedCountFractions
Summarize Continuous Observations in Explicit Groups	SummarizeGroupedValues
Nearest-Target Distances Summarised per Cell Set	SummarizeNearestDistances
Voronoi Territory Tiles of the Cells in a Field	TerritoryTiles
Manuscript 'ggplot2' Theme	ThemeManuscript
Typeset Figure Text	TypesetLabel
Variance Explained by Principal Components	VarianceExplained
Violin Plot of Marker Expression	ViolinPlot
Write a Figure from a Specification	WriteFigure

Package: phenoscapR 0.2.0.9001

phenoscapR: Read, Analyse, and Visualise Single-Cell Spatial Biology Data

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