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
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
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
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
+
+
+
2019-03-03
+
New features:
+
+Analysis app optionally creates tabular summaries and heatmap visualizations of nearest neighbor distance and count within radius for all phenotype pairs.
+Component levels report includes pair plots of component vs component for each source image.
+
+
Bug fixes:
+
+Component levels report
+Write CSV files to the export directory, not its parent.
+Fix height of “Pixel intensity by component” charts.
+Consolidate merged files
+Fix to recognize “Annotation ID” as the field name.
+Analyze consolidated data
+Update for dplyr 0.8 to fix #N/A values in Total lines of Cell Counts, Cell Percents and Cell Density sheets
+Clean up chart output
+“All” tissue category is last in charts which have it, same as “Total”.
+Fix “Cell Count” axis label
+Fix legend in H-Score chart - “name repair” in readxl version 1.2.0 created unexpected column names which were shown in the legend.
+
+
@@ -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 @@
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.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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 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_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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
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.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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 @@
+
+
+
+
+
+
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+
+Write a "count within" summary to an Excel workbook — write_count_within_sheet • phenoptrReports
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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.
+
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+
+
See also
+
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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 @@
+
+
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+
Write a nearest neighbor summary to an Excel workbook — write_nearest_neighbor_summary_sheet • phenoptrReports
+
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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
+
+
+
+
+
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+
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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
- worksheet_path
+ workbook_path
Path to an Excel file containing sheets written
by write_counts_sheet , etc.
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