Reference

All functions

aggregateNeighbors()

Function to aggregate all neighbors of each cell.

binAcrossPixels()

Aggregate consecutive pixels per single-metal spot

buildSpatialGraph()

Builds an interaction graph based on the cells' locations

countInteractions()

Summarizes cell-cell interactions within grouping levels (e.g. images)

detectCommunity()

Detect the spatial community of each cell

detectSpatialContext()

Detect the spatial context of each cell based on its neighborhood

filterPixels()

Filter pixels based on their assigned masses

filterSpatialContext()

Filter spatial contexts

findBorderCells()

Find cells at the image border

minDistToCells()

Function to calculate minimal distance to cells of interest

patchDetection()

Function to detect patches containing defined cell types

patchSize()

Function to compute the area of c3ll patches

plotSpatial()

Visualizes the spatial locations and interactions of cells

plotSpatialContext()

Plot spatial context graph

plotSpotHeatmap()

Summarizes and visualizes the pixel intensities per spot and channel

readImagefromTXT()

Reads one or multiple .txt files into a CytoImageList object

readSCEfromTXT()

Generates a SingleCellExperiment from .txt files

read_cpout()

Reads in single-cell data generated by the ImcSegmentationPipeline

read_steinbock()

Reads in single-cell data generated by the steinbock pipeline

show_cpout_features()

Display all features measured by CellProfiler.

testInteractions()

Tests if cell types interact more or less frequently than random