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

aggregated_nn_data_frameDump the nearest neighbor data that was extracted
as.data.frameGet the dataframe from a normalized nearest neighbor object.
binned_gated_nn_data_frameExtract and dump nearest neighbor raw data
collapse_markersThis function collapses two markers into one, and reruns the...
compare_normalized_nearest_neighborCompare distances between two markers to a reference marker.
Coordinate-classClass to represent a single imaging coordinate
counts_data_frameDataFrame from all the counts per frame
counts_per_mm2_data_frameDataFrame from all the counts on a per mm2 basis...
counts_per_mm2_sample_data_frameDataFrame from all the counts on a per mm2 basis per sample
counts_sample_data_frameDataFrame from all the counts per frame
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_counts_data_frameDataFrame from all the interaction counts on a per mm2 basis...
interaction_counts_sample_data_frameDataFrame from all the interaction counts on a per mm2 basis...
interaction_mapsPlot interaction maps for all samples
interactions_sample_data_frameDataFrame from all the counts on a per mm2 basis per sample
IrisSpatialFeatures_dataExample IrisSpatialFeatures dataset
IrisSpatialFeatures-packageIrisSpatialFeatures: A package to extract spatial features...
neighbor_ray_plotPlot nearest neighbor ray plots for each samples
nn_comparison_dataframeCompare nearest neighbors by a data.frame
nn_data_frameExtract and dump nearest neighbor raw data
NNN-classClass to represent a normalized nearest neighbor.
NNN_Compare-classClass to represent a comparison of two markers to a...
nn.testCalculate Nearest Neighbor for testing outputs
normal_nearest_neighborExtract the distance to each nearest neighbor for specified...
normal_nearest_neighbor_sampleExtract the distance to each nearest neighbor for specified...
normal_nearest_neighbor_sample_onceExtract the distance to each nearest neighbor for specified...
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_nnnPlot the normalized nearest neighbor (called internally)
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 June 15, 2018, 4:50 a.m.