Man pages for gusef/Iris
A package to extract spatial features based on multiplex IF images

as.data.frameRead inForm output and store it in an IrisSpatialFeatures...
collapse_markersThis function collapses two markers into one, and reruns the...
Coordinate-classClass to represent a single imaging coordinate
extract_featuresExtract all spatial features
extract_interactionsExtract interactions between all cell-types
extract_maskRead inForm output from a single coordinate
extract_nearest_neighborExtract the distance to each nearest neighbor for each...
extract_proximityRun a proximity analysis on all samples. There are two modes...
extract_ROIMethod that reduces the current dataset to a specific region...
feature_selectionFunction to extract all numeric features
get_all_interactionsGet all interactions between all cell-types
get_all_nearest_neighborsGet the nearest neighbor for each cell-type
get_all_proximitiesGet all proximity data for all cell-types in a sample
get_count_ratiosGet ratio of counts between two markers
get_counts_per_mm2Get all the counts on a per mm2 basis
get_counts_per_mm2_noncollapsedGet all the counts on a per mm2 basis non-collapsed
get_interactionsGet interactions for a specific marker
get_nearest_neighborsGet the nearest neighbor for a specified cell-type
get_proximitiesGet proximity data for a given cell-type
ImageSet-classClass to represent an imaging dataset.
interaction_mapsPlot interaction maps for all samples
IrisSpatialFeatures_dataExample IrisSpatialFeatures dataset
IrisSpatialFeatures-packageIrisSpatialFeatures: A package to extract spatial features...
neighbor_ray_plotPlot nearest neighbor ray plots for each samples
overview_plotPlot all coordinates in a given dataset
plotPlot all frames of an IrisSpatialFeatures ImageSet object.
plot_interactionsInteraction summary plot for all cell-types and all samples...
plot_nearest_neighborPlot average nearest neighbor barplots for two cell types....
plot_proximitiesPlot proximity analysis data
raw_data-classClass to represent the raw data that is output by inForm
rayplot_single_coordinatePlot nearest neighbor ray plots for a single coordinate
read_rawRead inForm output and store it in an IrisSpatialFeatures...
Sample-classAn S3 class to represent a single imaging sample with...
threshold_datasetThis function reads the manually determined thresholds of...
gusef/Iris documentation built on Nov. 8, 2017, 12:04 p.m.