diff --git a/DESCRIPTION b/DESCRIPTION index 08a872a..a64b4ac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.2.8.9000 -Date: 2020-05-18 +Version: 0.2.9 +Date: 2020-08-22 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), @@ -10,7 +10,7 @@ Authors@R: c( Copyright: Akoya Biosciences Description: Creates diagnostic and summary reports from inForm data. Language: en-US -Depends: R (>= 3.5.0) +Depends: R (>= 3.6.0) License: Zlib | file LICENSE Encoding: UTF-8 LazyData: true @@ -20,22 +20,22 @@ Imports: formattable (>= 0.2), forcats, fs, - ggplot2 (>= 3.0.0), + ggplot2 (>= 3.2.0), jpeg, knitr, magrittr, miniUI (>= 0.1.1), openxlsx, - phenoptr (> 0.2.7), + phenoptr (>= 0.2.8), png, - purrr, + purrr (>= 0.3), RColorBrewer, - readr, + readr (>= 1.2.1), readxl (>= 1.2.0), rlang (>= 0.4.0), rmarkdown, scales, - shiny (>= 0.13), + shiny (>= 1.3.2), shinydashboard, stringr, tibble (>= 2.0.0), @@ -53,7 +53,7 @@ Remotes: akoyabio/tiff, hms-dbmi/UpSetR Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.1 Suggests: ggridges, rstudioapi, diff --git a/NEWS.md b/NEWS.md index 0560693..cf4b2af 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# phenoptrReports 0.2.8.9000 +# phenoptrReports 0.2.9 +**2020-08-22** Analysis addin: - Nearest neighbors and count within are computed per tissue category and diff --git a/docs/404.html b/docs/404.html index 9b94a68..43b4782 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -159,7 +159,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index fc0d24a..f5077b9 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -178,7 +178,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index bb87064..0ba523d 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -93,13 +93,13 @@ -
+

Analyzing inForm data

Kent Johnson

-

2020-05-18

+

2020-09-22

Source: vignettes/analysis.Rmd @@ -235,7 +235,7 @@

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/analysis_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/analysis_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000..ca349fd --- /dev/null +++ b/docs/articles/analysis_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index 60af556..9c35c01 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -93,13 +93,13 @@ -
+

Consolidating inForm data

Kent Johnson

-

2020-05-18

+

2020-09-22

Source: vignettes/consolidation.Rmd @@ -153,13 +153,13 @@

Select input files

Click the “Browse Input” button in the “Select merge data files” section of the GUI. Use the file selection dialog to select your inForm merge data files. If the files are in multiple directories, click the Browse button multiple times to select them.

-

+

Select output directory

Click the “Browse Output” button in the “Select output directory” section of the GUI. Use the directory selection dialog to create a new directory to contain the output files.

-

+

@@ -210,7 +210,7 @@

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/consolidation_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/consolidation_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000..ca349fd --- /dev/null +++ b/docs/articles/consolidation_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index 50c07b2..c7757ed 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -164,7 +164,7 @@

Tutorials

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/spatial_map_viewer.html b/docs/articles/spatial_map_viewer.html index 87a0ccb..20e5d96 100644 --- a/docs/articles/spatial_map_viewer.html +++ b/docs/articles/spatial_map_viewer.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -93,13 +93,13 @@ -
+

Viewing nearest neighbors

Kent Johnson

-

2020-05-18

+

2020-09-22

Source: vignettes/spatial_map_viewer.Rmd @@ -205,7 +205,7 @@

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/spatial_map_viewer_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/spatial_map_viewer_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000..ca349fd --- /dev/null +++ b/docs/articles/spatial_map_viewer_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index 7404199..ac53d2d 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -93,13 +93,13 @@ -
+

Unmixing quality report

Kent Johnson

-

2020-05-18

+

2020-09-22

Source: vignettes/unmixing_quality_report.Rmd @@ -161,7 +161,7 @@

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/articles/unmixing_quality_report_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/unmixing_quality_report_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 0000000..ca349fd --- /dev/null +++ b/docs/articles/unmixing_quality_report_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/authors.html b/docs/authors.html index 2e5aef7..3431948 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -166,7 +166,7 @@

Authors

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/index.html b/docs/index.html index 942a04d..7ffbd98 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -211,7 +211,7 @@

Developers

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/news/index.html b/docs/news/index.html index ca16322..c638f74 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -140,6 +140,21 @@

Changelog

Source: NEWS.md
+
+

+phenoptrReports 0.2.9

+

2020-08-22

+

Analysis addin:

+ +

Spatial map viewer addin:

+ +

phenoptrReports 0.2.8

@@ -496,7 +511,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c01e592..1273238 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -244,14 +244,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a { .ref-index th {font-weight: normal;} -.ref-index td {vertical-align: top;} +.ref-index td {vertical-align: top; min-width: 100px} .ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} .ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} .ref-arguments .name {width: 20%;} .ref-arguments .desc {width: 80%;} diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 3bf0c00..1dd0974 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,12 +1,12 @@ pandoc: 2.7.3 -pkgdown: 1.5.1 +pkgdown: 1.6.1 pkgdown_sha: ~ articles: analysis: analysis.html consolidation: consolidation.html spatial_map_viewer: spatial_map_viewer.html unmixing_quality_report: unmixing_quality_report.html -last_built: 2020-05-18T18:01Z +last_built: 2020-09-22T19:27Z urls: reference: http://akoyabio.github.io/phenoptrReports/reference article: http://akoyabio.github.io/phenoptrReports/articles diff --git a/docs/reference/addin_10_merge.html b/docs/reference/addin_10_merge.html index 2b7b44b..39f93ce 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -77,7 +77,7 @@ phenoptrReports - 0.2.8 + 0.2.9
@@ -175,7 +175,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index 0cc896c..9ca6a88 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -171,7 +171,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index db2aa00..d37e21c 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -167,7 +167,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/addin_35_spatial_map_viewer.html b/docs/reference/addin_35_spatial_map_viewer.html index b1d74c7..9685f75 100644 --- a/docs/reference/addin_35_spatial_map_viewer.html +++ b/docs/reference/addin_35_spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -171,7 +171,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index f27caa5..48876d4 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -177,7 +177,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index 15c6e2c..9474717 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -171,7 +171,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html index 42db9d1..c68f131 100644 --- a/docs/reference/choose_directory.html +++ b/docs/reference/choose_directory.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -146,7 +146,7 @@

Cross-platform choose directory function.

Cross-platform choose directory function.

- 
choose_directory(caption = "Select folder", default = "")
+ 
choose_directory(caption = "Select folder", default = "")

Arguments

@@ -180,7 +180,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html index 9b97f07..8b5ac82 100644 --- a/docs/reference/choose_files.html +++ b/docs/reference/choose_files.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Cross-platform choose files function

choose_files(
-  caption = "Select files",
-  default = "",
-  multi = TRUE,
-  filters = NULL
+  caption = "Select files",
+  default = "",
+  multi = TRUE,
+  filters = NULL
 )

Arguments

@@ -194,7 +194,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index a19375a..02223e0 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -153,9 +153,9 @@

Create a component levels report for multiplex samples

component_levels_report(
-  export_path = NULL,
-  quantiles = 0.999,
-  export_data = FALSE
+  export_path = NULL,
+  quantiles = 0.999,
+  export_data = FALSE
 )

Arguments

@@ -198,7 +198,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 911a5c8..c8dc4eb 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -149,11 +149,11 @@

Compute cell densities from counts and tissue area

compute_density_from_cell_summary(
-  counts,
-  summary_path,
-  tissue_categories,
-  pixels_per_micron = getOption("phenoptr.pixels.per.micron"),
-  .by = "Slide ID"
+  counts,
+  summary_path,
+  tissue_categories,
+  pixels_per_micron = getOption("phenoptr.pixels.per.micron"),
+  .by = "Slide ID"
 )

Arguments

@@ -215,7 +215,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index bb3004f..a93a853 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -148,7 +148,7 @@

Compute cell densities from counts and tissue area

a table of tissue areas.

- 
compute_density_from_table(counts, areas, tissue_categories, .by = "Slide ID")
+ 
compute_density_from_table(counts, areas, tissue_categories, .by = "Slide ID")

Arguments

@@ -206,7 +206,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index 05ccedb..a483499 100644 --- a/docs/reference/compute_h_score.html +++ b/docs/reference/compute_h_score.html @@ -6,7 +6,7 @@ -Compute H-Score for a single marker aggregated by <code>.by</code> — compute_h_score • phenoptrReports +Compute H-Score for a single marker aggregated by .by — compute_h_score • phenoptrReports @@ -39,7 +39,7 @@ - + @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -146,7 +146,7 @@

Compute H-Score for a single marker aggregated by .by

Parameters are directly provided.

- 
compute_h_score(csd, measure, tissue_categories, thresholds, .by = "Slide ID")
+ 
compute_h_score(csd, measure, tissue_categories, thresholds, .by = "Slide ID")

Arguments

@@ -207,7 +207,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index dc08437..564ae30 100644 --- a/docs/reference/compute_h_score_from_score_data.html +++ b/docs/reference/compute_h_score_from_score_data.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,11 +147,11 @@

Compute H-Score based on parameters in a score data file

compute_h_score_from_score_data(
-  csd,
-  score_path,
-  tissue_categories = NULL,
-  .by = "Slide ID",
-  phenotype = NULL
+  csd,
+  score_path,
+  tissue_categories = NULL,
+  .by = "Slide ID",
+  phenotype = NULL
 )

Arguments

@@ -212,7 +212,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index 36450b2..d0dcbb2 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -150,7 +150,7 @@

Compute mean expression of cells for a single phenotype and marker.

Report the mean expression of the high-expressing cells.

- 
compute_mean_expression(csd, phenotype, param, percentile = NULL, count = NULL)
+ 
compute_mean_expression(csd, phenotype, param, percentile = NULL, count = NULL)

Arguments

@@ -215,7 +215,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index e317576..4d6ce22 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -149,13 +149,13 @@

Compute mean expression of cells for multiple phenotypes and markers.

compute_mean_expression_many(
-  csd,
-  phenotypes,
-  params,
-  tissue_categories = NULL,
-  percentile = NULL,
-  count = NULL,
-  .by = "Slide ID"
+  csd,
+  phenotypes,
+  params,
+  tissue_categories = NULL,
+  percentile = NULL,
+  count = NULL,
+  .by = "Slide ID"
 )

Arguments

@@ -246,7 +246,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 9b66bfa..2194882 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -146,7 +146,7 @@

Compute positivity of a single phenotype

Compute positivity of a single phenotype

- 
compute_positivity(csd, phenotype, positivity)
+ 
compute_positivity(csd, phenotype, positivity)

Arguments

@@ -202,7 +202,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index 2c450fa..08df90e 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Compute positivity of multiple phenotypes

compute_positivity_many(
-  csd,
-  phenotypes,
-  positivity_pairs,
-  tissue_categories = NULL
+  csd,
+  phenotypes,
+  positivity_pairs,
+  tissue_categories = NULL
 )

Arguments

@@ -211,7 +211,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/consolidate_and_summarize_cell_seg_data.html b/docs/reference/consolidate_and_summarize_cell_seg_data.html index b056bde..3d4d957 100644 --- a/docs/reference/consolidate_and_summarize_cell_seg_data.html +++ b/docs/reference/consolidate_and_summarize_cell_seg_data.html @@ -76,7 +76,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -154,9 +154,9 @@

Consolidate cell seg data files from parallel projects 
consolidate_and_summarize_cell_seg_data(
-  csd_files,
-  output_dir,
-  update_progress = NULL
+  csd_files,
+  output_dir,
+  update_progress = NULL
 )

Arguments

@@ -205,7 +205,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index 5f2d905..633cc9b 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -150,7 +150,7 @@

Count phenotypes per slide and tissue category

each Slide ID.

- 
count_phenotypes(csd, phenotypes, tissue_categories, .by = "Slide ID")
+ 
count_phenotypes(csd, phenotypes, tissue_categories, .by = "Slide ID")

Arguments

@@ -210,7 +210,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/count_within_summary.html b/docs/reference/count_within_summary.html index a65717a..1b6534b 100644 --- a/docs/reference/count_within_summary.html +++ b/docs/reference/count_within_summary.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -153,12 +153,13 @@

Summarize "count within" distances

count_within_summary(
-  csd,
-  radii,
-  phenotypes = NULL,
-  categories = NA,
-  details_path = NULL,
-  .by = "Slide ID"
+  csd,
+  radii,
+  phenotypes = NULL,
+  categories = NA,
+  details_path = NULL,
+  .by = "Slide ID",
+  extra_cols = NULL
 )

Arguments

@@ -181,17 +182,23 @@

Arg

- + - + + + + +
categories

Optional list of tissue categories to compute within.

Optional list of tissue categories to compute within. If +omitted or NA, all cells will be included.
details_path

If present, path to save a tab-separated table with -nearest-neighbor data for each cell.

If present, path to save tab-separated tables with +count within data for each cell.
.by

Column to aggregate by
extra_cols

The names of extra columns to include in the detailed +results.

Value

@@ -202,10 +209,11 @@

Details

If details_path is provided, this will save a table with one row per cell and columns for each phenotype and radius giving -the count of cells of that type within that distance. The detail table -is computed without regard to tissue category so it may not exactly -match the summary table. Details are only saved if the akoyabio/rtree -package is available.

+the count of cells of that type within that distance.

+

Note: If categories is NA or includes NA, the "All" tissue category in +the results will include all cells in csd. If categories does not include +NA, the "All" tissue category will include only cells in the provided +categories.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index e67b01f..0663eb5 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -150,7 +150,7 @@

Convert a count table to fractional percents

tissue category.

- 
counts_to_percents(counts)
+ 
counts_to_percents(counts)

Arguments

@@ -194,7 +194,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 17556f3..cad7f92 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -505,7 +505,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index f1c257d..b92d185 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -150,7 +150,7 @@

Merge inForm output from multiple fields.

does not include the ability to review and reject individual fields.

- 
merge_cell_seg_files(base_path, update_progress = NULL, recursive = FALSE)
+ 
merge_cell_seg_files(base_path, update_progress = NULL, recursive = FALSE)

Arguments

@@ -186,7 +186,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/nearest_neighbor_map.html b/docs/reference/nearest_neighbor_map.html index ffcb2f1..12abfa2 100644 --- a/docs/reference/nearest_neighbor_map.html +++ b/docs/reference/nearest_neighbor_map.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -149,15 +149,15 @@

Make a nearest neighbor map for a single field

nearest_neighbor_map(
-  csd,
-  field_name,
-  export_path,
-  phenos,
-  color1,
-  color2,
-  show_as = c("from_to", "to_from", "mutual", "none"),
-  dot_size = 3,
-  add_logo = TRUE
+  csd,
+  field_name,
+  export_path,
+  phenos,
+  color1,
+  color2,
+  show_as = c("from_to", "to_from", "mutual", "none"),
+  dot_size = 3,
+  add_logo = TRUE
 )

Arguments

@@ -200,7 +200,7 @@

Arg

Value

-

Returns a list containing two items:

+

Returns a list containing two items:

plot

The plot, a ggplot object.

data

A tibble containing the data used to create the line @@ -224,7 +224,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html index 3f21af5..48f076a 100644 --- a/docs/reference/nearest_neighbor_summary.html +++ b/docs/reference/nearest_neighbor_summary.html @@ -41,7 +41,13 @@ +for each .by in csd and each pair of phenotypes in phenotypes. +Statistics are computed separately for each category in categories +and, if multiple categories are provided, once for all included cells. +Note: If categories is NA or includes NA, the "All" tissue category in +the results will include all cells in csd. If categories does not include +NA, the "All" tissue category will include only cells in the provided +categories." /> @@ -73,7 +79,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -145,14 +151,22 @@

Summarize nearest neighbor distances

Computes summary nearest neighbor statistics (mean, median, etc) -for each .by in csd and each pair of phenotypes in phenotypes.

+for each .by in csd and each pair of phenotypes in phenotypes. +Statistics are computed separately for each category in categories +and, if multiple categories are provided, once for all included cells. +Note: If categories is NA or includes NA, the "All" tissue category in +the results will include all cells in csd. If categories does not include +NA, the "All" tissue category will include only cells in the provided +categories.

nearest_neighbor_summary(
-  csd,
-  phenotypes = NULL,
-  details_path = NULL,
-  .by = "Slide ID"
+  csd,
+  phenotypes = NULL,
+  categories = NA,
+  details_path = NULL,
+  .by = "Slide ID",
+  extra_cols = NULL
 )

Arguments

@@ -167,22 +181,33 @@

Arg

+ + + + - + + + + +
phenotypes

Optional list of phenotypes to include. If omitted, will use unique_phenotypes(csd).

categories

Optional list of tissue categories to compute within. If +omitted or NA, all cells will be included.
details_path

If present, path to save a tab-separated table with -nearest-neighbor data for each cell.

If present, path to save a tab-separated table +for each tissue category containing +nearest-neighbor data for each cell in the tissue category.
.by

Column to aggregate by
extra_cols

The names of extra columns to include in the detailed +results.

Value

A data frame with summary statistics for each phenotype pair -in each Slide ID.

+in each Slide ID for each tissue category.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index abcdf1c..bd42898 100644 --- a/docs/reference/order_by_slide_and_tissue_category.html +++ b/docs/reference/order_by_slide_and_tissue_category.html @@ -78,7 +78,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -156,7 +156,7 @@

Order a data frame by slide ID and tissue category, putting the "Total" category in the proper place.

- 
order_by_slide_and_tissue_category(d, tissue_categories, .by = "Slide ID")
+ 
order_by_slide_and_tissue_category(d, tissue_categories, .by = "Slide ID")

Arguments

@@ -194,7 +194,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/spatial_map_viewer.html b/docs/reference/spatial_map_viewer.html index e546233..bb00c40 100644 --- a/docs/reference/spatial_map_viewer.html +++ b/docs/reference/spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -151,7 +151,7 @@

Run the spatial map viewer with the given data for a GUI front-end to this function.

- 
spatial_map_viewer(csd_path, export_path)
+ 
spatial_map_viewer(csd_path, export_path)

Arguments

@@ -188,7 +188,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index 5735ccd..deb5eb3 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -148,7 +148,7 @@

Split a phenotype column

into multiple columns, one for each single phenotype.

- 
split_phenotypes(csd)
+ 
split_phenotypes(csd)

Arguments

@@ -183,7 +183,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index 6df9a8c..46c06e5 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -152,7 +152,7 @@

Create an unmixing quality report for simplex samples

the source directory.

- 
unmixing_quality_report(export_path = NULL)
+ 
unmixing_quality_report(export_path = NULL)

Arguments

@@ -185,7 +185,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index c835e92..d67a78b 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -146,7 +146,7 @@

Create an UpSet plot showing the phenotype combinations present in data.

See http://caleydo.org/tools/upset/ for an explanation of the plot.

- 
upset_plot(csd, expected = NULL)
+ 
upset_plot(csd, expected = NULL)

Arguments

@@ -181,7 +181,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html index 6ebf1d9..994abc7 100644 --- a/docs/reference/write_count_within_sheet.html +++ b/docs/reference/write_count_within_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -149,10 +149,10 @@

Write a "count within" summary to an Excel workbook

write_count_within_sheet(
-  wb,
-  stats,
-  sheet_name = "Count Within",
-  sheet_title = "Count of cells within the specified radius"
+  wb,
+  stats,
+  sheet_name = "Count Within",
+  sheet_title = "Count of cells within the specified radius"
 )

Arguments

@@ -203,7 +203,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index 68d9124..05c606d 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Write a cell counts table to an Excel workbook

write_counts_sheet(
-  wb,
-  counts,
-  sheet_name = "Cell Counts",
-  sheet_title = "Cell Counts per Phenotype"
+  wb,
+  counts,
+  sheet_name = "Cell Counts",
+  sheet_title = "Cell Counts per Phenotype"
 )

Arguments

@@ -202,7 +202,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index 06ddb04..0850c31 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Write a density table to an Excel workbook

write_density_sheet(
-  wb,
-  densities,
-  sheet_name = "Cell Densities",
-  sheet_title = "Cell Densities (cells/mm2)"
+  wb,
+  densities,
+  sheet_name = "Cell Densities",
+  sheet_title = "Cell Densities (cells/mm2)"
 )

Arguments

@@ -203,7 +203,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index 06eea12..ce30ee3 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Write an expression table to an Excel workbook

write_expression_sheet(
-  wb,
-  exprs,
-  sheet_name = "Mean Expression",
-  sheet_title = "Mean Expression"
+  wb,
+  exprs,
+  sheet_name = "Mean Expression",
+  sheet_title = "Mean Expression"
 )

Arguments

@@ -203,7 +203,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index f0833a5..555f6f1 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,11 +147,11 @@

Write an H-Score table to an Excel workbook

write_h_score_sheet(
-  wb,
-  h_score,
-  sheet_name = "H-Score",
-  sheet_title = NULL,
-  marker = NULL
+  wb,
+  h_score,
+  sheet_name = "H-Score",
+  sheet_title = NULL,
+  marker = NULL
 )

Arguments

@@ -209,7 +209,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_nearest_neighbor_summary_sheet.html b/docs/reference/write_nearest_neighbor_summary_sheet.html index 38edf25..6eea7d4 100644 --- a/docs/reference/write_nearest_neighbor_summary_sheet.html +++ b/docs/reference/write_nearest_neighbor_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -149,10 +149,10 @@

Write a nearest neighbor summary to an Excel workbook

write_nearest_neighbor_summary_sheet(
-  wb,
-  stats,
-  sheet_name = "Nearest Neighbors",
-  sheet_title = "Nearest Neighbor Distances for Phenotype Pairs (microns)"
+  wb,
+  stats,
+  sheet_name = "Nearest Neighbors",
+  sheet_title = "Nearest Neighbor Distances for Phenotype Pairs (microns)"
 )

Arguments

@@ -203,7 +203,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index 26535ff..5b5acb8 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Write a cell percent table to an Excel workbook

write_percents_sheet(
-  wb,
-  percents,
-  sheet_name = "Cell Percents",
-  sheet_title = "Percentage of Total Cells"
+  wb,
+  percents,
+  sheet_name = "Cell Percents",
+  sheet_title = "Percentage of Total Cells"
 )

Arguments

@@ -202,7 +202,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index 122a852..5bd1777 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -147,10 +147,10 @@

Write a plot to an Excel workbook

write_plot_sheet(
-  wb,
-  plot,
-  sheet_name = "Phenotypes",
-  sheet_title = "All combinations of phenotypes in all slides"
+  wb,
+  plot,
+  sheet_name = "Phenotypes",
+  sheet_title = "All combinations of phenotypes in all slides"
 )

Arguments

@@ -201,7 +201,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_session_info.html b/docs/reference/write_session_info.html index 878be83..8e93cdd 100644 --- a/docs/reference/write_session_info.html +++ b/docs/reference/write_session_info.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -148,7 +148,7 @@

Write session info to a file

if it is available, otherwise utils::sessionInfo() is used.

- 
write_session_info(path)
+ 
write_session_info(path)

Arguments

@@ -178,7 +178,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index 4dd54cc..f80b89e 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -80,7 +80,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -163,13 +163,13 @@

Write a single sheet with formatting common to all sheets.

write_sheet(
-  wb,
-  d,
-  sheet_name,
-  sheet_title,
-  header_col,
-  keepNA = TRUE,
-  addGrid = TRUE
+  wb,
+  d,
+  sheet_name,
+  sheet_title,
+  header_col,
+  keepNA = TRUE,
+  addGrid = TRUE
 )

Arguments

@@ -223,7 +223,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index e66e3c7..0f3dd4e 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -151,11 +151,11 @@

Create summary charts from the results of an analysis

write_summary_charts(
-  workbook_path,
-  output_path,
-  .by = "Slide ID",
-  max_slides_per_plot = 20,
-  max_heatmaps_per_plot = 8
+  workbook_path,
+  output_path,
+  .by = "Slide ID",
+  max_slides_per_plot = 20,
+  max_heatmaps_per_plot = 8
 )

Arguments

@@ -202,7 +202,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index 57dc73c..3700bf3 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -149,10 +149,10 @@

Create a summary report for a cell seg data file

write_summary_report(
-  csd_path = NULL,
-  csd = NULL,
-  dataset_name = NULL,
-  output_path
+  csd_path = NULL,
+  csd = NULL,
+  dataset_name = NULL,
+  output_path
 )

Arguments

@@ -192,7 +192,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index b3e0b0b..7e02cc8 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.8 + 0.2.9 @@ -148,7 +148,7 @@

Write a summary table to an Excel workbook

a sheet in an Excel workbook.

- 
write_summary_sheet(wb, summary_table, sheet_name = "Slide Summary")
+ 
write_summary_sheet(wb, summary_table, sheet_name = "Slide Summary")

Arguments

@@ -194,7 +194,7 @@

Contents

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 1.6.1.

diff --git a/man/count_within_summary.Rd b/man/count_within_summary.Rd index f0982f2..c560a9c 100644 --- a/man/count_within_summary.Rd +++ b/man/count_within_summary.Rd @@ -24,10 +24,11 @@ count_within_summary( will use \code{unique_phenotypes(csd)}. Counts are computed for all pairs of phenotypes.} -\item{categories}{Optional list of tissue categories to compute within.} +\item{categories}{Optional list of tissue categories to compute within. If +omitted or \code{NA}, all cells will be included.} -\item{details_path}{If present, path to save a tab-separated table with -nearest-neighbor data for each cell.} +\item{details_path}{If present, path to save tab-separated tables with +count within data for each cell.} \item{.by}{Column to aggregate by} @@ -47,8 +48,10 @@ summary calculation. \details{ If \code{details_path} is provided, this will save a table with one row per cell and columns for each phenotype and radius giving -the count of cells of that type within that distance. The detail table -is computed without regard to tissue category so it may not exactly -match the summary table. Details are only saved if the \code{akoyabio/rtree} -package is available. +the count of cells of that type within that distance. + +Note: If \code{categories} is \code{NA} or includes \code{NA}, the "All" tissue category in +the results will include all cells in \code{csd}. If \code{categories} does not include +\code{NA}, the "All" tissue category will include only cells in the provided +categories. } diff --git a/man/nearest_neighbor_summary.Rd b/man/nearest_neighbor_summary.Rd index eccdc72..41b0136 100644 --- a/man/nearest_neighbor_summary.Rd +++ b/man/nearest_neighbor_summary.Rd @@ -7,6 +7,7 @@ nearest_neighbor_summary( csd, phenotypes = NULL, + categories = NA, details_path = NULL, .by = "Slide ID", extra_cols = NULL @@ -19,8 +20,12 @@ nearest_neighbor_summary( \item{phenotypes}{Optional list of phenotypes to include. If omitted, will use \code{unique_phenotypes(csd)}.} -\item{details_path}{If present, path to save a tab-separated table with -nearest-neighbor data for each cell.} +\item{categories}{Optional list of tissue categories to compute within. If +omitted or \code{NA}, all cells will be included.} + +\item{details_path}{If present, path to save a tab-separated table +for each tissue category containing +nearest-neighbor data for each cell in the tissue category.} \item{.by}{Column to aggregate by} @@ -29,9 +34,15 @@ results.} } \value{ A data frame with summary statistics for each phenotype pair -in each Slide ID. +in each Slide ID for each tissue category. } \description{ Computes summary nearest neighbor statistics (mean, median, etc) for each \code{.by} in \code{csd} and each pair of phenotypes in \code{phenotypes}. +Statistics are computed separately for each category in \code{categories} +and, if multiple categories are provided, once for all included cells. +Note: If \code{categories} is \code{NA} or includes \code{NA}, the "All" tissue category in +the results will include all cells in \code{csd}. If \code{categories} does not include +\code{NA}, the "All" tissue category will include only cells in the provided +categories. }