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

PXL file database

PixelDB: PXL database class

Visualization

CellCountPlot(): Plot cell counts per group

MoleculeRankPlot(): Edge 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

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

Data processing

NormalizeMPX() superseded: Normalize MPX data

KeepLargestComponent(): Keep largest component

RemoveCellGraphs(): Remove CellGraphs

LoadCellGraphs(): Load CellGraphs

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

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

Sequencing saturation

sequencing_saturation(): Calculate Sequencing Saturation

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

downsample_to_parquet(): Filter an edgelist by downsampling read counts

lcc_sizes(): Calculate the sizes of the LCCs from an edgelist

lcc_curve() experimental: Compute LCC sizes for downsampled edgelists

Cell Annotation

AnnotateCells(): Automatic annotation of cell types

Color themes

color_discrete_pixelgen() color_sequential_pixelgen() color_divergent_pixelgen(): Pixelgen ggplot2 color themes

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

theme_pixelgen(): Pixelgen theme

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

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