Files in akoyabio/phenoptr
inForm Helper Functions
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
.lintr
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/average_counts.R
R/average_counts_rtree.R
R/count_touching_cells.R
R/count_touching_cells_fast.R
R/data.R
R/density_at_distance.R
R/density_bands.R
R/distance_funcs.R
R/helpers.R
R/phenoptr.R
R/read_cell_seg_data.R
R/read_components.R
R/read_composites.R
R/read_maps.R
R/select_rows.R
R/spatial_distribution_report.R
R/spatial_helpers.R
R/zzz.R
README.md
TODO
_pkgdown.yml
codecov.yml
data/sample_cell_seg_data.rda
docs/404.html
docs/LICENSE-text.html
docs/articles/computing_distances.html
docs/articles/computing_distances_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/computing_distances_files/figure-html/unnamed-chunk-10-1.png
docs/articles/computing_distances_files/figure-html/unnamed-chunk-11-1.png
docs/articles/computing_distances_files/figure-html/unnamed-chunk-13-1.png
docs/articles/computing_distances_files/figure-html/unnamed-chunk-7-1.png
docs/articles/computing_distances_files/figure-html/unnamed-chunk-8-1.png
docs/articles/computing_distances_files/header-attrs-2.11/header-attrs.js
docs/articles/computing_distances_files/header-attrs-2.3/header-attrs.js
docs/articles/computing_distances_files/header-attrs-2.8/header-attrs.js
docs/articles/computing_distances_files/header-attrs-2.9/header-attrs.js
docs/articles/find_and_count_touching_cells.R
docs/articles/find_and_count_touching_cells.html
docs/articles/find_and_count_touching_cells_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/find_and_count_touching_cells_files/header-attrs-2.11/header-attrs.js
docs/articles/find_and_count_touching_cells_files/header-attrs-2.3/header-attrs.js
docs/articles/find_and_count_touching_cells_files/header-attrs-2.8/header-attrs.js
docs/articles/find_and_count_touching_cells_files/header-attrs-2.9/header-attrs.js
docs/articles/index.html
docs/articles/reading_image_files.R
docs/articles/reading_image_files.html
docs/articles/reading_image_files_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/reading_image_files_files/figure-html/display_map-1.png
docs/articles/reading_image_files_files/figure-html/plotting-1.png
docs/articles/reading_image_files_files/figure-html/show_composite-1.png
docs/articles/reading_image_files_files/header-attrs-2.11/header-attrs.js
docs/articles/reading_image_files_files/header-attrs-2.3/header-attrs.js
docs/articles/reading_image_files_files/header-attrs-2.8/header-attrs.js
docs/articles/reading_image_files_files/header-attrs-2.9/header-attrs.js
docs/articles/reading_tables.html
docs/articles/reading_tables_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/reading_tables_files/figure-html/ggplot2-1.png
docs/articles/reading_tables_files/figure-html/ggplot2-2.png
docs/articles/reading_tables_files/header-attrs-2.11/header-attrs.js
docs/articles/reading_tables_files/header-attrs-2.3/header-attrs.js
docs/articles/reading_tables_files/header-attrs-2.8/header-attrs.js
docs/articles/reading_tables_files/header-attrs-2.9/header-attrs.js
docs/articles/selecting_cells.R
docs/articles/selecting_cells.html
docs/articles/selecting_cells_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/selecting_cells_files/header-attrs-2.11/header-attrs.js
docs/articles/selecting_cells_files/header-attrs-2.3/header-attrs.js
docs/articles/selecting_cells_files/header-attrs-2.8/header-attrs.js
docs/articles/selecting_cells_files/header-attrs-2.9/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/compute_all_nearest_distance.html
docs/reference/count_touching_cells.html
docs/reference/count_touching_cells_fast.html
docs/reference/count_within.html
docs/reference/count_within_batch.html
docs/reference/count_within_detail.html
docs/reference/count_within_many.html
docs/reference/count_within_many_impl.html
docs/reference/count_within_many_impl_dist.html
docs/reference/count_within_many_impl_rtree.html
docs/reference/density_at_distance-1.png
docs/reference/density_at_distance-2.png
docs/reference/density_at_distance.html
docs/reference/density_bands-1.png
docs/reference/density_bands.html
docs/reference/distance_matrix.html
docs/reference/field_column.html
docs/reference/figures/Akoya.png
docs/reference/find_nearest_distance.html
docs/reference/find_nearest_distance_dist.html
docs/reference/find_nearest_distance_rtree.html
docs/reference/get_field_info.html
docs/reference/get_map_path.html
docs/reference/index.html
docs/reference/list_cell_seg_files.html
docs/reference/make_phenotype_column.html
docs/reference/make_ppp-1.png
docs/reference/make_ppp-2.png
docs/reference/make_ppp.html
docs/reference/parse_composite_info.html
docs/reference/parse_names_and_colors.html
docs/reference/parse_phenotypes.html
docs/reference/parse_tissue_description.html
docs/reference/phenoptr-package.html
docs/reference/phenotype_columns.html
docs/reference/phenotype_names.html
docs/reference/plot_diverging.html
docs/reference/readTIFFDirectory.html
docs/reference/read_cell_seg_data.html
docs/reference/read_components.html
docs/reference/read_composite_info.html
docs/reference/read_composites.html
docs/reference/read_field_info.html
docs/reference/read_maps.html
docs/reference/sample_cell_seg_data.html
docs/reference/select_rows.html
docs/reference/spatial_distribution_report.html
docs/reference/split_and_trim.html
docs/reference/split_by_slash.html
docs/reference/split_quoted.html
docs/reference/stop_if_multiple_fields.html
docs/reference/subset_distance_matrix.html
docs/reference/unique_phenotypes.html
docs/reference/validate_phenotype_definitions.html
docs/reference/validate_phenotypes.html
docs/sitemap.xml
inst/WORDLIST
inst/extdata/sample/Set4_1-6plex_[16142,55840]_binary_seg_maps.tif
inst/extdata/sample/Set4_1-6plex_[16142,55840]_cell_seg_data.txt
inst/extdata/sample/Set4_1-6plex_[16142,55840]_cell_seg_data_summary.txt
inst/extdata/sample/Set4_1-6plex_[16142,55840]_component_data.tif
inst/extdata/sample/Set4_1-6plex_[16142,55840]_composite_image.jpg
inst/rmd/SpatialDistributionReport.Rmd
man/compute_all_nearest_distance.Rd
man/count_touching_cells.Rd
man/count_touching_cells_fast.Rd
man/count_within.Rd
man/count_within_batch.Rd
man/count_within_detail.Rd
man/count_within_many.Rd
man/count_within_many_impl.Rd
man/count_within_many_impl_dist.Rd
man/count_within_many_impl_rtree.Rd
man/density_at_distance.Rd
man/density_bands.Rd
man/distance_matrix.Rd
man/field_column.Rd
man/figures/Akoya.png
man/find_nearest_distance.Rd
man/find_nearest_distance_dist.Rd
man/find_nearest_distance_rtree.Rd
man/get_field_info.Rd
man/get_map_path.Rd
man/list_cell_seg_files.Rd
man/make_phenotype_column.Rd
man/make_ppp.Rd
man/parse_composite_info.Rd
man/parse_names_and_colors.Rd
man/parse_phenotypes.Rd
man/parse_tissue_description.Rd
man/phenoptr-package.Rd
man/phenotype_columns.Rd
man/phenotype_names.Rd
man/plot_diverging.Rd
man/readTIFFDirectory.Rd
man/read_cell_seg_data.Rd
man/read_components.Rd
man/read_composite_info.Rd
man/read_composites.Rd
man/read_field_info.Rd
man/read_maps.Rd
man/sample_cell_seg_data.Rd
man/select_rows.Rd
man/spatial_distribution_report.Rd
man/split_and_trim.Rd
man/split_quoted.Rd
man/stop_if_multiple_fields.Rd
man/subset_distance_matrix.Rd
man/unique_phenotypes.Rd
man/validate_phenotype_definitions.Rd
man/validate_phenotypes.Rd
phenoptr.Rproj
tests/testthat.R
tests/testthat/test_average_counts.R
tests/testthat/test_count_touching_cells.R
tests/testthat/test_data/ColorAssignments.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_0_cell_seg_data.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_1_cell_seg_data.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_binary_seg_maps.tif
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_cell_seg_data.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_cell_seg_data_summary.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_comma_cell_seg_data.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_comma_cell_seg_data_summary.txt
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_component_data.tif
tests/testthat/test_data/FIHC4__0929309_HP_IM3_2_composite_image.jpg
tests/testthat/test_data/FIHC4__0929309_HP_IM3_3_cell_seg_data.txt
tests/testthat/test_data/consolidated/FIHC4_consolidated_merge_cell_seg_data.txt
tests/testthat/test_data/consolidated/Set4_1-6plex_[16142,55840]_cons_cell_seg_data.txt
tests/testthat/test_data/merge/FIHC4_merge_cell_seg_data.txt
tests/testthat/test_density.R
tests/testthat/test_distance_funcs.R
tests/testthat/test_parse_phenotypes.R
tests/testthat/test_read_cell_seg_data.R
tests/testthat/test_read_composites.R
tests/testthat/test_read_images.R
tests/testthat/test_results/FIHC4__0929309_HP_IM3_2_Helper_T_touch_B.tif
tests/testthat/test_results/FIHC4__0929309_HP_IM3_2_Helper_T_touch_Cytotoxic_T.tif
tests/testthat/test_results/count_within.csv
tests/testthat/test_select_rows.R
tests/testthat/test_spatial_distribution_report.R
tests/testthat/test_spatial_helpers.R
tools/CountTouchingCellsExample.R
tools/Helpers.R
tools/floodFillBenchmark.R
tools/lazyeval_vs_map_as_formula.R
vignettes/computing_distances.Rmd
vignettes/find_and_count_touching_cells.Rmd
vignettes/reading_image_files.Rmd
vignettes/reading_image_files_files/figure-html/display_map-1.png
vignettes/reading_image_files_files/figure-html/plotting-1.png
vignettes/reading_image_files_files/figure-html/show_composite-1.png
vignettes/reading_tables.Rmd
vignettes/selecting_cells.Rmd
vignettes/touch_counts.csv
