Package index • pixelatorR

Function reference

Load data

ReadMPX_Seurat(): Load data from PXL file into a Seurat object
ReadMPX_counts(): Read a count matrix from a pxl file
ReadMPX_item() ReadMPX_polarization() ReadMPX_colocalization() ReadMPX_edgelist(): Read an MPX data item
ReadMPX_arrow_edgelist(): Read edgelists from a PXL file containing MPX data
ReadMPX_layouts(): Load layouts from an PXL file containing MPX data
ReadMPX_metadata(): Read metadata from a PXL file
ReadPNA_Seurat(): Load data from PNA PXL file into a Seurat object
ReadPNA_counts(): Read a count matrix from a PXL file with PNA data
ReadPNA_edgelist(): Load the edge list from a PNA PXL file
ReadPNA_proximity(): Load the Proximity scores table from a PNA PXL file
ReadPNA_layouts(): Load layouts from a PNA PXL file
ReadPNA_metadata(): Read metadata from a PNA PXL file
read_pbmc_reference(): Read PBMC cell annotation reference

PXL file database

PixelDB: PXL database class
get_duckdb_config(): Fetches the config values to be used with DuckDB

Visualization

CellCountPlot(): Plot cell counts per group
MoleculeRankPlot(): Molecule Rank Plot
EdgeRankPlot() deprecated: Edge Rank Plot
TauPlot(): Plot UMIs per UPIa for quality control
DensityScatterPlot(): Create a density scatter / pseudocolor plot.
AbundanceColocalizationPlot(): Create an abundance/colocalization scatterplot
Plot2DGraph(): Plot 2D graph layouts
Plot2DGraphM(): Plot multiple markers on multiple graphs
Plot3DGraph(): Plot 3D graph layouts

Graph layouts

ComputeLayout(): Compute a graph layout
layout_with_weighted_pmds(): Weighted PMDS
layout_with_coarsened_pmds(): Coarsened pMDS
center_layout_coordinates() normalize_layout_coordinates() project_layout_coordinates_on_unit_sphere(): Layout Coordinates Utility Functions
render_rotating_layout() experimental: Create a rotating 3D layout video
scale_layout(): Scale layout coordinates
fast_pmds(): Fast pMDS implementation using RSpectra

Data processing

NormalizeMPX() superseded: Normalize MPX data
KeepLargestComponent(): Keep largest component
RemoveCellGraphs(): Remove CellGraphs
LoadCellGraphs(): Load CellGraphs
CalculateDispersion(): Calculate dispersion of components
ComputeProximityScores(): Compute proximity scores
SequenceSaturationCurve(): Simulate Sequencing Saturation Curve
approximate_edge_saturation(): Compute approximate edge saturation
approximate_node_saturation(): Compute approximate node saturation
approximate_saturation_curve(): Compute approximate saturation curve
sequencing_saturation(): Calculate Sequencing Saturation
downsample_to_parquet(): Downsample edgelist and export to parquet files
lcc_curve() experimental: Compute LCC curve for downsampled edgelists
lcc_sizes(): Compute LCC sizes from downsampled edgelists
isotype_pls(): Partial Least Squares Regression for background factor regression
cos_dist(): Calculate cosine distances between two sets of coordinates
pack_2bits() unpack_2bits(): Encode/decode DNA sequences

Differential analysis

RunDAA(): Differential analysis (abundance)
RunDPA(): Differential analysis (polarity)
RunDCA(): Differential analysis (colocalization)
DifferentialProximityAnalysis(): Differential analysis of proximity scores
ColocalizationHeatmap(): Plot a colocalization heatmap

Cell type annotation

AnnotateCells(): Automatic annotation of cell types

Proximity scores

PolarizationScoresToAssay(): Convert polarization score table to an Assay or Assay5
ColocalizationScoresToAssay(): Convert colocalization score table to an Assay or Assay5
ProximityScoresToAssay(): Convert proximity score table to an Assay or Assay5
FilterProximityScores(): Filter proximity scores
SummarizeProximityScores(): Summarize proximity scores

Doublet detection

FindAnnoyNeighbors(): Approximate nearest neighbors using Annoy
SimulateDoublets(): Simulate doublets
PredictDoublets() experimental: Predict doublets in a Seurat object

Patch analysis

identify_markers_for_patch_analysis(): Identify population-specific markers for patch detection
patch_detection() experimental: Supervised patch detection

CellGraphAssay(5), PNAAssay(5) and CellGraph methods

RenameCells(<CellGraphAssay>) show(<CellGraphAssay>) subset(<CellGraphAssay>) merge(<CellGraphAssay>): CellGraphAssay Methods
RenameCells(<CellGraphAssay5>) show(<CellGraphAssay5>) subset(<CellGraphAssay5>) merge(<CellGraphAssay5>) JoinLayers(<CellGraphAssay5>): CellGraphAssay5 Methods
RenameCells(<PNAAssay>) show(<PNAAssay>) subset(<PNAAssay>) merge(<PNAAssay>): PNAAssay Methods
RenameCells(<PNAAssay5>) show(<PNAAssay5>) subset(<PNAAssay5>) merge(<PNAAssay5>) JoinLayers(<PNAAssay5>): PNAAssay5 Methods
RenameCells(<MPXAssay>) show(<MPXAssay>) subset(<MPXAssay>) merge(<MPXAssay>): MPXAssay Methods
CreateCellGraphAssay(): Create a CellGraphAssay object
CreateCellGraphAssay5(): Create a CellGraphAssay5 object
CreatePNAAssay(): Create a PNAAssay object
CreatePNAAssay5(): Create a PNAAssay5 object
CellGraphs() `CellGraphs<-`(): CellGraphs
PolarizationScores() `PolarizationScores<-`(): PolarizationScores
ColocalizationScores() `ColocalizationScores<-`(): ColocalizationScores
ProximityScores() `ProximityScores<-`(): ProximityScores
Edgelists(): Load edgelists
Normalize(): Normalize MPX or PNA data
FSMap() `FSMap<-`(): FS map
RestorePaths(): Restore PXL file paths
CellGraphData() `CellGraphData<-`(): Get and set CellGraph object data
as.CellGraphAssay(): Convert objects to a CellGraphAssay
as.CellGraphAssay5(): Convert objects to a CellGraphAssay5
as.PNAAssay(): Convert objects to a PNAAssay
as.PNAAssay5(): Convert objects to a PNAAssay5
CellGraph-class CellGraph: The CellGraph class
CreateCellGraphObject(): Create a CellGraph object

Graph functions

edgelist_to_simple_Anode_graph() deprecated: A-node projection
edgelist_to_simple_bipart_graph(): Create a simple bipartite graph from an edgelist
node_markers_counts() deprecated: Calculate antibody counts per A-node
color_by_marker() deprecated: Add node colors to a CellGraph
compute_transition_probabilities(): Compute transition probabilities
cos_distance_weights() prob_distance_weights() experimental: Calculate edge weights for pMDS
local_G(): Calculate Local G
expand_adjacency_matrix(): Expand an adjacency matrix to include higher-order neighborhoods

Export

WriteMPX_pxl_file() experimental: Export Seurat object MPX data to a PXL file

Classes

CellGraphAssay-class CellGraphAssay: The CellGraphAssay class
CellGraphAssay5-class CellGraphAssay5: The CellGraphAssay5 class
MPXAssay-class MPXAssay: MPXAssay class
PNAAssay-class PNAAssay: The PNAAssay class
PNAAssay5-class PNAAssay5: The PNAAssay5 class

Colors

PixelgenAccentColors(): Get Pixelgen accent colors
PixelgenGradient(): Get Pixelgen gradient colors
PixelgenPalette(): Get Pixelgen palette colors
Pixelgen_accent_colors: Pixelgen accent colors
show_accent_colors(): Show accent colors
color_discrete_pixelgen() color_sequential_pixelgen() color_divergent_pixelgen(): Pixelgen ggplot2 color themes
create_discrete_palette(): Create sample palette
theme_pixelgen(): Pixelgen theme
Pixelgen_cell_palette: Pixelgen cell type colors
heuristic_illumination(): Compute heuristic illumination for 3D layouts

Misc

pixelatorR_options: Global Options in pixelatorR
pixelatorR-package: pixelatorR: Data Structures, Data Processing Tools and Visualization Tools for MPX Single Cell Data
minimal_mpx_pxl_file(): Five Cells MPX Test data
minimal_pna_pxl_file(): Five Cells PNA Test data
show(<CellGraph>) subset(<CellGraph>): CellGraph Methods
RenameCells(<CellGraphAssay>) show(<CellGraphAssay>) subset(<CellGraphAssay>) merge(<CellGraphAssay>): CellGraphAssay Methods
inspect_pxl_file(): Inspect a PXL file with MPX data
pixelatorR_style(): The pixelatorR style
print(<pixelator_metadata>): Print method for pixelator_metadata
assert_single_value() assert_vector() assert_class() assert_mpx_assay() assert_pna_assay() assert_pixel_assay() assert_within_limits() assert_function() assert_file_exists() assert_file_ext() assert_x_in_y() assert_single_values_are_different() assert_singles_match() assert_length() assert_max_length() assert_vectors_x_y_length_equal() assert_unique() assert_col_class() assert_col_in_data() assert_non_empty_object() assert_is_one_of() assert_different() assert_vectors_match() assert_valid_color(): Type check helpers
export_plot(): Save a ggplot2 plot to one or more file formats with options for size and directory creation.