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 .pxl files

ReadMPX_layouts() experimental: Load layouts from an PXL file

ReadMPX_metadata(): Read metadata from a PXL file

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() experimental: Weighted PMDS

center_layout_coordinates() normalize_layout_coordinates() project_layout_coordinates_on_unit_sphere(): Layout Coordinates Utility Functions

Data processing

NormalizeMPX(): Normalize MPX data

KeepLargestComponent(): Keep largest component

RemoveCellGraphs(): Remove CellGraphs

LoadCellGraphs(): Load CellGraphs

Differential analysis

RunDAA(): Differential analysis (abundance)

RunDPA(): Differential analysis (polarity)

RunDCA(): Differential analysis (colocalization)

ColocalizationHeatmap(): Plot a colocalization heatmap

Seurat methods

PolarizationScoresToAssay(): Convert polarization score table to an Assay or Assay5

ColocalizationScoresToAssay(): Convert colocalization score table to an Assay or Assay5

CellGraphAssay(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(<MPXAssay>) show(<MPXAssay>) subset(<MPXAssay>) merge(<MPXAssay>): MPXAssay Methods

CreateCellGraphAssay(): Create a CellGraphAssay object

CreateCellGraphAssay5(): Create a CellGraphAssay5 object

CellGraphs() `CellGraphs<-`(): CellGraphs

PolarizationScores() `PolarizationScores<-`(): PolarizationScores

ColocalizationScores() `ColocalizationScores<-`(): ColocalizationScores

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

CellGraph-class CellGraph: The CellGraph class

CreateCellGraphObject(): Create a CellGraph object

Graph functions

edgelist_to_simple_Anode_graph(): A-node projection

edgelist_to_simple_bipart_graph(): Create a simple bipartite graph from an edgelist

node_markers_counts(): Calculate antibody counts per A-node

color_by_marker(): 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() experimental: Calculate Local G

Export

WriteMPX_pxl_file() experimental: Export Seurat object data to a .pxl file

Classes

CellGraphAssay-class CellGraphAssay: The CellGraphAssay class

CellGraphAssay5-class CellGraphAssay5: The CellGraphAssay5 class

MPXAssay-class MPXAssay: MPXAssay class

Misc

pixelatorR_options: Global Options in pixelatorR

pixelatorR-package: pixelatorR: Data Structures, Data Processing Tools and Visualization Tools for MPX Single Cell Data

pxl_dataset: Five Cells MPX Test data

show(<CellGraph>): Show method for CellGraph object

RenameCells(<CellGraphAssay>) show(<CellGraphAssay>) subset(<CellGraphAssay>) merge(<CellGraphAssay>): CellGraphAssay Methods

inspect_pxl_file(): Inspect a PXL file

pixelatorR_style(): The pixelatorR style

print(<pixelator_metadata>): Print method for pixelator_metadata

assert_single_value() assert_vector() assert_class() assert_mpx_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(): Type check helpers