From ca777d042e8549ff674e768fe451e96f4b2a6911 Mon Sep 17 00:00:00 2001 From: Kent Johnson Date: Fri, 10 May 2019 12:35:20 -0400 Subject: [PATCH] Update version to 0.2.0 and rebuild docs. --- DESCRIPTION | 6 +++--- NEWS.md | 5 +++-- 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 | 2 +- docs/news/index.html | 20 ++++++++++++++++++- .../reference/add_tissue_category_totals.html | 8 ++++++-- 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/cc_and.html | 2 +- docs/reference/check_phenotypes.html | 2 +- docs/reference/choose_directory.html | 2 +- docs/reference/choose_files.html | 2 +- docs/reference/component_levels_report.html | 2 +- .../compute_density_from_cell_summary.html | 11 +++++++--- .../reference/compute_density_from_table.html | 11 +++++++--- docs/reference/compute_h_score.html | 15 +++++++++----- .../compute_h_score_from_score_data.html | 8 ++++++-- docs/reference/compute_mean_expression.html | 2 +- .../compute_mean_expression_many.html | 18 +++++++++-------- docs/reference/compute_positivity.html | 2 +- docs/reference/compute_positivity_many.html | 2 +- ...nsolidate_and_summarize_cell_seg_data.html | 2 +- docs/reference/count_phenotypes.html | 8 ++++++-- docs/reference/count_within_summary.html | 8 ++++++-- docs/reference/counts_to_percents.html | 2 +- docs/reference/file_to_fluor.html | 2 +- docs/reference/function_exists.html | 2 +- docs/reference/index.html | 4 ++-- docs/reference/make_nested.html | 8 ++++++-- docs/reference/make_unique_names.html | 2 +- docs/reference/merge_cell_seg_files.html | 2 +- docs/reference/nearest_neighbor_summary.html | 13 ++++++++---- .../order_by_slide_and_tissue_category.html | 11 +++++++--- 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 | 2 +- docs/reference/write_count_within_sheet.html | 2 +- docs/reference/write_counts_sheet.html | 2 +- docs/reference/write_density_sheet.html | 2 +- docs/reference/write_expression_sheet.html | 2 +- docs/reference/write_h_score_sheet.html | 2 +- .../write_nearest_neighbor_summary_sheet.html | 2 +- docs/reference/write_percents_sheet.html | 2 +- docs/reference/write_plot_sheet.html | 2 +- docs/reference/write_session_info.html | 2 +- docs/reference/write_sheet.html | 2 +- docs/reference/write_summary_charts.html | 14 +++++++++++-- docs/reference/write_summary_report.html | 2 +- docs/reference/write_summary_sheet.html | 2 +- inst/WORDLIST | 2 ++ 61 files changed, 171 insertions(+), 93 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fe79365..3ec66b3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.1.7.9000 -Date: 2019-03-03 +Version: 0.2.0 +Date: 2019-05-10 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 (>= 0.1.6.9000), + phenoptr (>= 0.2.0), purrr, readr, readxl (>= 1.2.0), diff --git a/NEWS.md b/NEWS.md index 4c6deee..455e457 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# phenoptrReports 0.1.7.9000 +# phenoptrReports 0.2.0 +**2019-05-10** Analysis addin: - Add support for aggregation by a selectable column (#3). This allows @@ -12,7 +13,7 @@ Analysis addin: numeric Slide IDs. Bug fixes: -- Fix the way the analysis addin handles of special characters in Slide ID (#9). +- Fix the way the analysis addin handles special characters in Slide ID (#9). - Fix file chooser to work on RStudio Server. # phenoptrReports 0.1.7 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 7d5b1e2..c01f97c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index ede80e4..f99ce5a 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -94,7 +94,7 @@

Analyzing inForm data

Kent Johnson

-

2019-04-12

+

2019-05-10

Source: vignettes/analysis.Rmd diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index 8ad8846..c47de85 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -94,7 +94,7 @@

Consolidating inForm data

Kent Johnson

-

2019-04-12

+

2019-05-10

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index c679600..01b0b5e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index 0402780..e2c960b 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -94,7 +94,7 @@

Unmixing quality report

Kent Johnson

-

2019-04-12

+

2019-05-10

Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/authors.html b/docs/authors.html index de7191f..c9b28de 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/index.html b/docs/index.html index cc74528..9c6e887 100644 --- a/docs/index.html +++ b/docs/index.html @@ -30,7 +30,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/news/index.html b/docs/news/index.html index a290d4d..d37f451 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -126,6 +126,23 @@

Changelog

Source: NEWS.md +
+

+phenoptrReports 0.2.0

+

2019-05-10

+

Analysis addin:

+ +

Bug fixes:

+ +

phenoptrReports 0.1.7

@@ -293,6 +310,7 @@

Contents

    +
  • 0.2.0
  • 0.1.7
  • 0.1.6
  • 0.1.5
    • diff --git a/docs/reference/add_tissue_category_totals.html b/docs/reference/add_tissue_category_totals.html index 8b23efa..4cfc187 100644 --- a/docs/reference/add_tissue_category_totals.html +++ b/docs/reference/add_tissue_category_totals.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0
@@ -136,7 +136,7 @@

Add total rows to a data frame if there are multiple tissue categories.

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

Arguments

@@ -150,6 +150,10 @@

Arg

+ + + +
tissue_categories

The tissue categories of interest, ordered.
.by

Column to aggregate by

Value

diff --git a/docs/reference/addin_10_merge.html b/docs/reference/addin_10_merge.html index 3687f13..de730b2 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -68,7 +68,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index 72475e8..a7daebc 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index dc888b4..67f7e79 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index 585278e..2a6dc3f 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index f43b044..f44feda 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/cc_and.html b/docs/reference/cc_and.html index 87a0a9b..987f4e3 100644 --- a/docs/reference/cc_and.html +++ b/docs/reference/cc_and.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/check_phenotypes.html b/docs/reference/check_phenotypes.html index 6279a0d..87ef88c 100644 --- a/docs/reference/check_phenotypes.html +++ b/docs/reference/check_phenotypes.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html index 6cef25c..be15d21 100644 --- a/docs/reference/choose_directory.html +++ b/docs/reference/choose_directory.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html index 1e4a463..cd193dc 100644 --- a/docs/reference/choose_files.html +++ b/docs/reference/choose_files.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index 8da6b51..f24b10e 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 984e007..9d22107 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -139,14 +139,15 @@

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"))
+ pixels_per_micron = getOption("phenoptr.pixels.per.micron"), + .by = "Slide ID")

Arguments

- @@ -163,6 +164,10 @@

Arg

+ + + +
counts

A data frame with columns for Slide ID, Tissue Category, +

A data frame with columns for .by, Tissue Category, and counts, such as the output of count_phenotypes.
pixels_per_micron

Conversion factor to microns.
.by

Column to aggregate by

Value

diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index 3cb5039..7179ea9 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -138,14 +138,15 @@

Compute cell densities from counts and tissue area

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

Arguments

- @@ -158,6 +159,10 @@

Arg

+ + + +
counts

A data frame with columns for Slide ID, Tissue Category, +

A data frame with columns for .by, Tissue Category, and counts, such as the output of count_phenotypes.

A character vector of tissue category names of interest.
.by

Column to aggregate by

Value

diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index 9ba843a..c0da5dd 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 Slide ID — compute_h_score • phenoptrReports +Compute H-Score for a single marker aggregated by <code>.by</code> — compute_h_score • phenoptrReports @@ -30,7 +30,7 @@ - + @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -125,7 +125,7 @@
-

Compute H-Score for a single marker aggregated by Slide ID

+

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

Source: R/positivity.R
@@ -136,7 +136,8 @@

Compute H-Score for a single marker aggregated by Slide ID

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

Arguments

@@ -158,6 +159,10 @@

Arg

+ + + +
thresholds

Optional three element vector with the threshold values.
.by

Column to aggregate by

Value

diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index e920c81..e59657e 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 - 0.1.7 + 0.2.0
@@ -137,7 +137,7 @@

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

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

Arguments

@@ -155,6 +155,10 @@

Arg

+ + + +

optionally specify tissue categories of interest. If not given, tissue categories are taken from the score file.
.by

Column to aggregate by

Value

diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index be01673..5fd8f1b 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index 50a5185..ccda95d 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -139,7 +139,8 @@

Compute mean expression of cells for multiple phenotypes and markers.

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

Arguments

@@ -148,7 +149,7 @@

Arg

+!!.by and Tissue Category.

@@ -178,6 +179,10 @@

Arg all cells matching the phenotype are used and the result is the overall mean expression.

+ + + +
csd

Cell seg data to use. This should already have been filtered for the slides or fields of interest. It may already be nested by -Slide ID and Tissue Category.
phenotypes
.by

Column to aggregate by

Value

@@ -194,11 +199,8 @@

Details percentile=-.1 would give the expression of the lowest-expressing decile.

By default, this function aggregates by Slide ID and Tissue Category. -To compute mean expression by a different aggregate, pass a data frame nested by -the desired columns. For example, to aggregate by field and tissue -category, pass -tidyr::nest(csd, -`Slide ID`, -`Sample Name`, -`Tissue Category`) -as the csd parameter.

+To compute mean expression by a different aggregate, pass a column name in +the .by parameter.

To aggregate over all cells, include "Total Cells"=NA as one of the phenotypes.

diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 49dc26d..4999c18 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index f0be95c..3fddc9a 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/consolidate_and_summarize_cell_seg_data.html b/docs/reference/consolidate_and_summarize_cell_seg_data.html index 5563e27..fda0c9f 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 - 0.1.7 + 0.2.0 diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index 4be32c2..97cbfb3 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -140,7 +140,7 @@

Count phenotypes per slide and tissue category

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

Arguments

@@ -162,6 +162,10 @@

Arg

+ + + +

A character vector of tissue category names of interest.
.by

Column to aggregate by

Value

diff --git a/docs/reference/count_within_summary.html b/docs/reference/count_within_summary.html index b788066..9ca0d3b 100644 --- a/docs/reference/count_within_summary.html +++ b/docs/reference/count_within_summary.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -143,7 +143,7 @@

Summarize "count within" distances

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

Arguments

@@ -172,6 +172,10 @@

Arg

+ + + +

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

Column to aggregate by

Value

diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index a90be9b..2ac1e6c 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/file_to_fluor.html b/docs/reference/file_to_fluor.html index 3d23d6e..633d3ca 100644 --- a/docs/reference/file_to_fluor.html +++ b/docs/reference/file_to_fluor.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/function_exists.html b/docs/reference/function_exists.html index 891b7d0..135d6ec 100644 --- a/docs/reference/function_exists.html +++ b/docs/reference/function_exists.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index eeaec62..05d9cb8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -216,7 +216,7 @@

compute_h_score()

-

Compute H-Score for a single marker aggregated by Slide ID

+

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

diff --git a/docs/reference/make_nested.html b/docs/reference/make_nested.html index 627455b..cbd8631 100644 --- a/docs/reference/make_nested.html +++ b/docs/reference/make_nested.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -141,7 +141,7 @@

Make a nested data frame with one row per Slide ID and - 
make_nested(csd, tissue_categories = NULL)
+ 
make_nested(csd, tissue_categories = NULL, .by = "Slide ID")

Arguments

@@ -155,6 +155,10 @@

Arg

+ + + +

If provided, the result will be filtered and nested by the provided categories.
.by

Column to aggregate by

Value

diff --git a/docs/reference/make_unique_names.html b/docs/reference/make_unique_names.html index 3a18652..3c79493 100644 --- a/docs/reference/make_unique_names.html +++ b/docs/reference/make_unique_names.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index 750c314..a66a335 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html index 08201c7..3680287 100644 --- a/docs/reference/nearest_neighbor_summary.html +++ b/docs/reference/nearest_neighbor_summary.html @@ -33,7 +33,7 @@ +for each .by in csd and each pair of phenotypes in phenotypes." /> @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -134,11 +134,12 @@

Summarize nearest neighbor distances

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

+for each .by in csd and each pair of phenotypes in phenotypes.

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

Arguments

@@ -158,6 +159,10 @@

Arg

+ + + +

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

Column to aggregate by

Value

diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index 9767738..e84e32d 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 - 0.1.7 + 0.2.0 @@ -146,19 +146,24 @@

Order a data frame by slide ID and tissue category, putting the - 
order_by_slide_and_tissue_category(d, tissue_categories)
+ 
order_by_slide_and_tissue_category(d, tissue_categories,
+  .by = "Slide ID")

Arguments

- + + + + +
d

A data frame with Slide ID and Tissue Category columns

A data frame with .by and Tissue Category columns
tissue_categories

A vector of category names in the desired order
.by

First column to sort by

Value

diff --git a/docs/reference/process_singleplex_image.html b/docs/reference/process_singleplex_image.html index d4d6dcc..33242fe 100644 --- a/docs/reference/process_singleplex_image.html +++ b/docs/reference/process_singleplex_image.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index e414d9a..c741270 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index fe99a04..a813f12 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/upset_data.html b/docs/reference/upset_data.html index f1f568b..ddb0119 100644 --- a/docs/reference/upset_data.html +++ b/docs/reference/upset_data.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index 2ca62b0..833d4a3 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/validate_phenotype_definitions.html b/docs/reference/validate_phenotype_definitions.html index 4f724af..6107d5e 100644 --- a/docs/reference/validate_phenotype_definitions.html +++ b/docs/reference/validate_phenotype_definitions.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html index 8acccf3..d048acc 100644 --- a/docs/reference/write_count_within_sheet.html +++ b/docs/reference/write_count_within_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index b381fe5..97dae1c 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index 4cf807b..f7b205e 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index a0a1dc5..151d295 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index be4a00d..ec98a24 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_nearest_neighbor_summary_sheet.html b/docs/reference/write_nearest_neighbor_summary_sheet.html index 805e01c..c117f8c 100644 --- a/docs/reference/write_nearest_neighbor_summary_sheet.html +++ b/docs/reference/write_nearest_neighbor_summary_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index b93c532..859b67a 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index fae94e3..2ce9fe6 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -63,7 +63,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_session_info.html b/docs/reference/write_session_info.html index a4b035f..ae2124e 100644 --- a/docs/reference/write_session_info.html +++ b/docs/reference/write_session_info.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index 8e6661b..f0763ca 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -69,7 +69,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index 6333198..452dc92 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.7 + 0.2.0 @@ -140,7 +140,8 @@

Create summary charts from the results of an analysis

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

Arguments

@@ -154,6 +155,15 @@

Arg

+ + + + + + + +
output_path

Path to write the resulting file.
.by

Name of the grouping parameter in the worksheets

max_slides_per_plot

Maximum number of slides or samples +to show on each plot

diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index a64d97d..0ff8c12 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index 64b7e09..c6cb3a9 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.7 + 0.2.0 diff --git a/inst/WORDLIST b/inst/WORDLIST index 6b91e9c..b0ca581 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -2,6 +2,7 @@ addin Addin Addins Akoya +akoyabio Autofluorescence BiocInstaller Biosciences @@ -31,6 +32,7 @@ quartile readxl RStudio seg +selectable singleplex Singleplex sn