# Methods for imaging mass cytometry data analysis

## Documentation for package ‘imcRtools’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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