From 1cb711800714f7f8767fb041905c8098b8e170fa Mon Sep 17 00:00:00 2001 From: Kent Johnson Date: Sun, 3 Mar 2019 15:01:19 -0500 Subject: [PATCH] Update to version 0.1.6 and rebuild docs. --- DESCRIPTION | 6 +- NEWS.md | 3 +- docs/LICENSE-text.html | 2 +- docs/articles/analysis.html | 4 +- docs/articles/consolidation.html | 4 +- docs/articles/index.html | 2 +- docs/articles/unmixing_quality_report.html | 4 +- docs/authors.html | 2 +- docs/index.html | 4 +- docs/news/index.html | 29 ++- .../reference/add_tissue_category_totals.html | 2 +- docs/reference/addin_10_merge.html | 2 +- docs/reference/addin_20_consolidate.html | 2 +- docs/reference/addin_30_analysis_app.html | 2 +- docs/reference/addin_40_unmixing_quality.html | 2 +- docs/reference/addin_50_component_levels.html | 2 +- docs/reference/check_phenotypes.html | 2 +- docs/reference/component_levels_report.html | 2 +- .../compute_density_from_cell_summary.html | 2 +- .../reference/compute_density_from_table.html | 2 +- docs/reference/compute_h_score.html | 2 +- .../compute_h_score_from_score_data.html | 2 +- docs/reference/compute_mean_expression.html | 2 +- .../compute_mean_expression_many.html | 2 +- docs/reference/compute_positivity.html | 2 +- docs/reference/compute_positivity_many.html | 2 +- ...nsolidate_and_summarize_cell_seg_data.html | 5 +- docs/reference/count_phenotypes.html | 2 +- docs/reference/count_within_summary.html | 204 +++++++++++++++++ docs/reference/counts_to_percents.html | 2 +- docs/reference/file_to_fluor.html | 2 +- docs/reference/index.html | 26 ++- docs/reference/make_nested.html | 2 +- docs/reference/make_unique_names.html | 2 +- docs/reference/merge_cell_seg_files.html | 4 +- docs/reference/nearest_neighbor_summary.html | 191 ++++++++++++++++ .../order_by_slide_and_tissue_category.html | 2 +- docs/reference/process_singleplex_image.html | 2 +- docs/reference/split_phenotypes.html | 2 +- docs/reference/unmixing_quality_report.html | 2 +- docs/reference/upset_data.html | 2 +- docs/reference/upset_plot.html | 2 +- .../validate_phenotype_definitions.html | 4 +- docs/reference/write_count_within_sheet.html | 204 +++++++++++++++++ docs/reference/write_counts_sheet.html | 6 +- docs/reference/write_density_sheet.html | 6 +- docs/reference/write_expression_sheet.html | 6 +- docs/reference/write_h_score_sheet.html | 6 +- .../write_nearest_neighbor_summary_sheet.html | 205 ++++++++++++++++++ docs/reference/write_percents_sheet.html | 6 +- docs/reference/write_plot_sheet.html | 6 +- docs/reference/write_sheet.html | 11 +- docs/reference/write_summary_charts.html | 6 +- docs/reference/write_summary_report.html | 2 +- docs/reference/write_summary_sheet.html | 6 +- docs/sitemap.xml | 11 +- 56 files changed, 957 insertions(+), 72 deletions(-) create mode 100644 docs/reference/count_within_summary.html create mode 100644 docs/reference/nearest_neighbor_summary.html create mode 100644 docs/reference/write_count_within_sheet.html create mode 100644 docs/reference/write_nearest_neighbor_summary_sheet.html diff --git a/DESCRIPTION b/DESCRIPTION index d1e5854..b997c14 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.1.5.9000 -Date: 2018-11-05 +Version: 0.1.6 +Date: 2019-03-03 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), @@ -22,7 +22,7 @@ Imports: magrittr, miniUI (>= 0.1.1), openxlsx, - phenoptr (> 0.1.4), + phenoptr (>= 0.1.5), purrr, readr, readxl, diff --git a/NEWS.md b/NEWS.md index 9126ab8..9be6a57 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# phenoptrReports 0.1.5.9000 +# phenoptrReports 0.1.6 +**2019-03-03** New features: - Analysis app optionally creates tabular summaries and heatmap visualizations diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 97ceb7c..68079aa 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index cb2ccbd..9380eb8 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -94,7 +94,7 @@

Analyzing inForm data

Kent Johnson

-

2019-01-25

+

2019-03-03

Source: vignettes/analysis.Rmd diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index c8feaa9..f6db5d9 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -94,7 +94,7 @@

Consolidating inForm data

Kent Johnson

-

2019-01-25

+

2019-03-03

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index b5ef1cc..c7c0c1e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index cbce508..a696d2f 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -94,7 +94,7 @@

Unmixing quality report

Kent Johnson

-

2019-01-25

+

2019-03-03

Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/authors.html b/docs/authors.html index eaf699d..df641b8 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/index.html b/docs/index.html index 6c6f10b..8f0a27d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -175,7 +175,7 @@

The most important input file is the consolidated data file from the consolidation step. Selecting a summary cell seg data file enables density calculations; selecting a score data file enables H-Score calculation.

To define the analysis, you select tissue categories, phenotypes, and markers of interest.

-

To create the finalreports, the analysis app writes and runs an R script. The script computes the aggregated statistics, writes them to an Excel workbook, and creates visualizations of the results in a Word document.

+

To create the final reports, the analysis app writes and runs an R script. The script computes the aggregated statistics, writes them to an Excel workbook, and creates visualizations of the results in a Word document.

For detailed instructions and requirements, see the Analyzing inForm data tutorial.

diff --git a/docs/news/index.html b/docs/news/index.html index 4f3123a..0a48013 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -126,6 +126,30 @@

Changelog

Source: NEWS.md +
+

+phenoptrReports 0.1.6

+

2019-03-03

+

New features:

+ +

Bug fixes:

+ +

phenoptrReports 0.1.5

@@ -200,7 +224,7 @@

2018-10-22

New features:

    -
  • Add version number, date stamp and doco link to generated script file #2
  • +
  • Add version number, date stamp and documentation link to generated script file #2
  • Add H-Score chart to the generated charts
  • Add Akoya logo to footer in chart report
@@ -225,6 +249,7 @@

Contents

diff --git a/docs/reference/addin_10_merge.html b/docs/reference/addin_10_merge.html index a79656a..ac4b45d 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -68,7 +68,7 @@ phenoptrReports - 0.1.5 + 0.1.6

diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index eca28b4..18a2829 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index 2b1450f..4752833 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index fc7d62c..5835ede 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index f049bfe..3ae930b 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/check_phenotypes.html b/docs/reference/check_phenotypes.html index 45f205d..267d152 100644 --- a/docs/reference/check_phenotypes.html +++ b/docs/reference/check_phenotypes.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index 9529af5..70f027b 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 08f4d89..8babdcb 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index ba8d59d..85baf4f 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index b2f1403..d8b92e5 100644 --- a/docs/reference/compute_h_score.html +++ b/docs/reference/compute_h_score.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index d9717da..dcfb944 100644 --- a/docs/reference/compute_h_score_from_score_data.html +++ b/docs/reference/compute_h_score_from_score_data.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index cd1b919..675ac1e 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index e08e000..c977b19 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 71bb487..aad0acc 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index 4fd2825..07a1b90 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/consolidate_and_summarize_cell_seg_data.html b/docs/reference/consolidate_and_summarize_cell_seg_data.html index e5535f5..2a19f6e 100644 --- a/docs/reference/consolidate_and_summarize_cell_seg_data.html +++ b/docs/reference/consolidate_and_summarize_cell_seg_data.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -172,7 +172,8 @@

Details

Write the consolidated data to Consolidated_data.txt in the output directory.

The -individual files must all have exactly the same Sample Name and Cell ID +individual files must all have exactly the same +Sample Name or Annotation ID and Cell ID columns. split_phenotypes is called to split the Phenotype columns.

diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index 0795027..d0e1923 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/count_within_summary.html b/docs/reference/count_within_summary.html new file mode 100644 index 0000000..13d96b6 --- /dev/null +++ b/docs/reference/count_within_summary.html @@ -0,0 +1,204 @@ + + + + + + + + +Summarize "count within" distances — count_within_summary • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+ + +
+ +

Computes summary "count within" statistics +for each Slide ID in csd and each pair of phenotypes in phenotypes. +See phenoptr::count_within() for details of the counts and the +summary calculation.

+ +
+ +
count_within_summary(csd, radii, phenotypes = NULL, categories = NULL)
+ +

Arguments

+ + + + + + + + + + + + + + + + + + +
csd

Cell seg data with Cell X Position, +Cell Y Position, field name and Phenotype columns.

radii

Vector of radii to search within.

phenotypes

Optional list of phenotypes to include. If omitted, +will use unique_phenotypes(csd). Counts are computed for all +pairs of phenotypes.

categories

Optional list of tissue categories to compute within.

+ +

Value

+ +

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

+ + +
+ +
+ +
+ + +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index d1a765c..2a357f0 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/file_to_fluor.html b/docs/reference/file_to_fluor.html index 2d55da3..3c95f1c 100644 --- a/docs/reference/file_to_fluor.html +++ b/docs/reference/file_to_fluor.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/index.html b/docs/reference/index.html index ac153a2..aa1d3e6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -259,6 +259,18 @@

count_phenotypes()

Count phenotypes per slide and tissue category

+ + + +

count_within_summary()

+ +

Summarize "count within" distances

+ + + +

nearest_neighbor_summary()

+ +

Summarize nearest neighbor distances

@@ -295,6 +307,12 @@

write_count_within_sheet()

+ +

Write a "count within" summary to an Excel workbook

+ +

write_density_sheet()

@@ -313,6 +331,12 @@

write_nearest_neighbor_summary_sheet()

+ +

Write a nearest neighbor summary to an Excel workbook

+ +

write_percents_sheet()

diff --git a/docs/reference/make_nested.html b/docs/reference/make_nested.html index 1f30f00..e7a1099 100644 --- a/docs/reference/make_nested.html +++ b/docs/reference/make_nested.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/make_unique_names.html b/docs/reference/make_unique_names.html index 1f69264..c4a65d6 100644 --- a/docs/reference/make_unique_names.html +++ b/docs/reference/make_unique_names.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index 494607e..49208f8 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -149,7 +149,7 @@

Arg base_path

Path to a directory containing files to merge. All -elegible files in this directory will be merged.

+eligible files in this directory will be merged.

update_progress diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html new file mode 100644 index 0000000..9165f36 --- /dev/null +++ b/docs/reference/nearest_neighbor_summary.html @@ -0,0 +1,191 @@ + + + + + + + + +Summarize nearest neighbor distances — nearest_neighbor_summary • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+ + +
+ +

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

+ +
+ +
nearest_neighbor_summary(csd, phenotypes = NULL)
+ +

Arguments

+ + + + + + + + + + +
csd

Cell seg data with Cell X Position, +Cell Y Position, field name and Phenotype columns.

phenotypes

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

+ +

Value

+ +

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

+ + +
+ +
+ +
+ + +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index edda401..be6eeaf 100644 --- a/docs/reference/order_by_slide_and_tissue_category.html +++ b/docs/reference/order_by_slide_and_tissue_category.html @@ -69,7 +69,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/process_singleplex_image.html b/docs/reference/process_singleplex_image.html index d171777..0e34f32 100644 --- a/docs/reference/process_singleplex_image.html +++ b/docs/reference/process_singleplex_image.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index f0a1ecd..55b4f9a 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index 1a7eb82..f32e2ff 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/upset_data.html b/docs/reference/upset_data.html index 7f72da5..a280eed 100644 --- a/docs/reference/upset_data.html +++ b/docs/reference/upset_data.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index c6a3502..d192462 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/validate_phenotype_definitions.html b/docs/reference/validate_phenotype_definitions.html index c7661c7..df9cbc5 100644 --- a/docs/reference/validate_phenotype_definitions.html +++ b/docs/reference/validate_phenotype_definitions.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -148,7 +148,7 @@

Arg pheno -

Text destription of a phenotype, +

Text description of a phenotype, for phenoptr::parse_phenotypes.

diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html new file mode 100644 index 0000000..eea8069 --- /dev/null +++ b/docs/reference/write_count_within_sheet.html @@ -0,0 +1,204 @@ + + + + + + + + +Write a "count within" summary to an Excel workbook — write_count_within_sheet • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+ + +
+ +

Write a formatted "count within" summary table to a +sheet in an Excel workbook.

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

Arguments

+ + + + + + + + + + + + + + + + + + +
wb

An openxlsx Workbook from openxlsx::createWorkbook

stats

A summary data frame.

sheet_name

Optional name for the worksheet.

sheet_title

Optional title header for the table.

+ +

See also

+ + + + +
+ +
+ +
+ + +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index af5c8da..c8ea504 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -163,9 +163,11 @@

Arg

See also

-

Other output functions: write_density_sheet, +

diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index 9c2d81c..a122a80 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -164,9 +164,11 @@

Arg

See also

-

Other output functions: write_counts_sheet, +

diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index 45c3ac3..ec145d1 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -164,9 +164,11 @@

Arg

See also

-

Other output functions: write_counts_sheet, +

diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index e926ce5..0bd6c94 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -164,9 +164,11 @@

Arg

See also

-

Other output functions: write_counts_sheet, +

diff --git a/docs/reference/write_nearest_neighbor_summary_sheet.html b/docs/reference/write_nearest_neighbor_summary_sheet.html new file mode 100644 index 0000000..26fecae --- /dev/null +++ b/docs/reference/write_nearest_neighbor_summary_sheet.html @@ -0,0 +1,205 @@ + + + + + + + + +Write a nearest neighbor summary to an Excel workbook — write_nearest_neighbor_summary_sheet • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+ + +
+ +

Write a formatted nearest neighbor summary table to a +sheet in an Excel workbook.

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

Arguments

+ + + + + + + + + + + + + + + + + + +
wb

An openxlsx Workbook from openxlsx::createWorkbook

stats

A summary data frame.

sheet_name

Optional name for the worksheet.

sheet_title

Optional title header for the table.

+ +

See also

+ + + + +
+ +
+ +
+ + +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index 21b9a8f..8e2ab45 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -163,10 +163,12 @@

Arg

See also

-

Other output functions: write_counts_sheet, +

diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index 8f9f0fe..0827f71 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -162,10 +162,12 @@

Arg

See also

-

Other output functions: write_counts_sheet, +

diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index 1dcfd1f..a81a3dc 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -69,7 +69,7 @@ phenoptrReports - 0.1.5 + 0.1.6
@@ -148,7 +148,8 @@

Write a single sheet with formatting common to all sheets.

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

Arguments

@@ -177,6 +178,12 @@

Arg

+ + + +
keepNA

If TRUE, NA values are written as #N/A; else they are blank.

addGrid

If TRUE, grid lines (and page breaks) are added based +on the tissue categories in the data. If FALSE, no grid lines are added +and page breaks are added where needed.

diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index 9424448..1affb80 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -140,13 +140,13 @@

Create summary charts from the results of an analysis

-
write_summary_charts(worksheet_path, output_path)
+
write_summary_charts(workbook_path, output_path)

Arguments

- + diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index b7f0d87..6b96d8f 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index cc23438..2055f5a 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.5 + 0.1.6 @@ -159,10 +159,12 @@

Arg

See also

-

Other output functions: write_counts_sheet, +

diff --git a/docs/sitemap.xml b/docs/sitemap.xml index befcd32..14f3103 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -61,7 +61,7 @@ http://akoyabio.github.io/phenoptrReports/reference/count_phenotypes.html - http://akoyabio.github.io/phenoptrReports/reference/field_column.html + http://akoyabio.github.io/phenoptrReports/reference/count_within_summary.html http://akoyabio.github.io/phenoptrReports/reference/file_to_fluor.html @@ -75,6 +75,9 @@ http://akoyabio.github.io/phenoptrReports/reference/merge_cell_seg_files.html + + http://akoyabio.github.io/phenoptrReports/reference/nearest_neighbor_summary.html + http://akoyabio.github.io/phenoptrReports/reference/order_by_slide_and_tissue_category.html @@ -99,6 +102,9 @@ http://akoyabio.github.io/phenoptrReports/reference/write_counts_sheet.html + + http://akoyabio.github.io/phenoptrReports/reference/write_count_within_sheet.html + http://akoyabio.github.io/phenoptrReports/reference/write_density_sheet.html @@ -108,6 +114,9 @@ http://akoyabio.github.io/phenoptrReports/reference/write_h_score_sheet.html + + http://akoyabio.github.io/phenoptrReports/reference/write_nearest_neighbor_summary_sheet.html + http://akoyabio.github.io/phenoptrReports/reference/write_percents_sheet.html
worksheet_pathworkbook_path

Path to an Excel file containing sheets written by write_counts_sheet, etc.