diff --git a/DESCRIPTION b/DESCRIPTION index 2f12609..f269491 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.2.5.9000 -Date: 2019-10-22 +Version: 0.2.6 +Date: 2020-02-25 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), diff --git a/NEWS.md b/NEWS.md index 7d676f7..01a142e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,12 +1,5 @@ -# phenoptrReports 0.2.5.9000 - -- Use the RStudio folder chooser when available, rather than the Windows - native chooser. The RStudio chooser is nicer and gives access to - network drives (#29). - -Merge addin: -- Fix a problem that caused data corruption when cell seg data is - formatted with comma as decimal separator (#31). +# phenoptrReports 0.2.6 +**2020-02-25** Analysis addin: - Don't require tissue segmentation in the inForm project (#4). @@ -19,6 +12,15 @@ Analysis addin: reported (#1). - Report missing / invalid values consistently as #N/A, never as #NUM. +Merge addin: +- Fix a problem that caused data corruption when cell seg data is + formatted with comma as decimal separator (#31). + +Misc: +- Use the RStudio folder chooser when available, rather than the Windows + native chooser. The RStudio chooser is nicer and gives access to + network drives (#29). + # phenoptrReports 0.2.5 **2019-10-22** diff --git a/docs/404.html b/docs/404.html index 57eda33..adafd49 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 0e996de..6f92a53 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -67,7 +67,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index 7c6b0c1..046b793 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -99,7 +99,7 @@

Analyzing inForm data

Kent Johnson

-

2019-10-22

+

2020-02-25

Source: vignettes/analysis.Rmd @@ -169,7 +169,7 @@

Slide ID prefix

-

The Slide IDs in your data file may contain prefix information that is not wanted in the final report. Any text you enter here will be removed from the start of the Slide IDs. The text can be either an exact match or a regular expression. In either case it will match from the start of the Slide ID.

+

The Slide IDs in your data file may contain prefix information that is not wanted in the final report. Any text you enter here will be removed from the start of the Slide IDs. The text can be either an exact match or a regular expression. Exact matches will match from the start of the Slide ID. Regular expressions will match anywhere in the Slide ID; to match only from the start, start the regular expression with ^.

Leave this field blank to use the existing Slide IDs unchanged.

@@ -186,6 +186,12 @@

+
+

+H-Score for individual phenotypes

+

If you selected a score summary file in the Files tab, the phenotype selections will include a “Score” checkbox. If this is checked, the generated report will include H-Score for the selected phenotype in addition to the H-Score for all cells.

+

+

Select options for spatial analysis

@@ -241,6 +247,7 @@

  • Define phenotypes and markers
    • +
  • H-Score for individual phenotypes
  • Select options for spatial analysis
  • Create reports
    • diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index ae16d9e..629eeb7 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.5 + 0.2.6

    @@ -99,7 +99,7 @@

    Consolidating inForm data

    Kent Johnson

    -

    2019-10-22

    +

    2020-02-25

    Source: vignettes/consolidation.Rmd diff --git a/docs/articles/figures/Phenotypes_with_score.png b/docs/articles/figures/Phenotypes_with_score.png new file mode 100644 index 0000000..6b37888 Binary files /dev/null and b/docs/articles/figures/Phenotypes_with_score.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 1daf575..f6185cd 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -67,7 +67,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/articles/spatial_map_viewer.html b/docs/articles/spatial_map_viewer.html index eae999f..77f220f 100644 --- a/docs/articles/spatial_map_viewer.html +++ b/docs/articles/spatial_map_viewer.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -99,7 +99,7 @@

    Viewing nearest neighbors

    Kent Johnson

    -

    2019-10-22

    +

    2020-02-25

    Source: vignettes/spatial_map_viewer.Rmd diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index 4a801a3..c906d7a 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -99,7 +99,7 @@

    Unmixing quality report

    Kent Johnson

    -

    2019-10-22

    +

    2020-02-25

    Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/authors.html b/docs/authors.html index 3f70041..a4892dd 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/index.html b/docs/index.html index 3a28816..1df9812 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/news/index.html b/docs/news/index.html index f088dd1..f67b38f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,7 +67,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -136,6 +136,27 @@

    Changelog

    Source: NEWS.md +
    +

    +phenoptrReports 0.2.6

    +

    2020-02-25

    +

    Analysis addin:

    + +

    Merge addin:

    + +

    Misc:

    + +

    phenoptrReports 0.2.5

    @@ -425,6 +446,7 @@

    Contents

      +
    • 0.2.6
    • 0.2.5
    • 0.2.4
    • 0.2.3
      • diff --git a/docs/reference/addin_10_merge.html b/docs/reference/addin_10_merge.html index 9a919da..88ee867 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.5 + 0.2.6
    diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index 5bf3534..4ee9650 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6

    diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index 7b44067..591fc4a 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/addin_35_spatial_map_viewer.html b/docs/reference/addin_35_spatial_map_viewer.html index ea329ea..9946784 100644 --- a/docs/reference/addin_35_spatial_map_viewer.html +++ b/docs/reference/addin_35_spatial_map_viewer.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index 56c01b9..62791c9 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index d7fd740..943539b 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html index a6fadf6..ac0eac7 100644 --- a/docs/reference/choose_directory.html +++ b/docs/reference/choose_directory.html @@ -69,7 +69,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html index c28a7e3..5611cac 100644 --- a/docs/reference/choose_files.html +++ b/docs/reference/choose_files.html @@ -69,7 +69,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -143,8 +143,12 @@

    Cross-platform choose files function

    Cross-platform choose files function

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

    Arguments

    diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index 156a6a2..157d40a 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -149,8 +149,11 @@

    Create a component levels report for multiplex samples

    the source directory.

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

    Arguments

    diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index e626547..1b4164b 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -145,9 +145,13 @@

    Compute cell densities from counts and tissue area

    read from a summary cell seg data file.

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

    Arguments

    @@ -182,15 +186,16 @@

    Value

    A data table with counts converted to density in \(cells / mm^2\).

    See also

    -

    Other aggregation functions: compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -145,8 +145,7 @@

    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

    @@ -178,15 +177,16 @@

    Value

    A data table with counts converted to density in \(cells / mm^2\).

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -143,8 +143,7 @@

    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

    @@ -179,15 +178,16 @@

    Value

    measure and thresholds.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -143,8 +143,12 @@

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

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

    Arguments

    @@ -174,15 +178,16 @@

    Value

    percents in each bin and the H-Score. See compute_h_score.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -147,8 +147,7 @@

    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

    @@ -187,15 +186,16 @@

    Value

    A data frame with columns for count and mean.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_positivity_many, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -145,9 +145,15 @@

    Compute mean expression of cells for multiple phenotypes and markers.

    report the mean expression of the given marker in the specified cells.

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

    Arguments

    @@ -211,15 +217,16 @@

    Details phenotypes.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -173,15 +173,16 @@

    Value

    and fraction (fraction of positive cells).

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +count_phenotypes(), +counts_to_percents()

    @@ -143,8 +143,12 @@

    Compute positivity of multiple phenotypes

    Compute positivity of multiple phenotypes

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

    Arguments

    @@ -178,15 +182,16 @@

    Value

    and percent for each element of positivity_pairs.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity, - count_phenotypes, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity(), +count_phenotypes(), +counts_to_percents()

    @@ -150,8 +150,11 @@

    Consolidate cell seg data files from parallel projects into a single file with separate columns for each phenotype.

    - 
    consolidate_and_summarize_cell_seg_data(csd_files, output_dir,
-  update_progress = NULL)
    + 
    consolidate_and_summarize_cell_seg_data(
+  csd_files,
+  output_dir,
+  update_progress = NULL
+)

    Arguments

    diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index b91d205..91a2f22 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -181,15 +181,16 @@

    Value

    counts for each requested phenotype, and total cells.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - counts_to_percents

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +counts_to_percents()

    @@ -149,8 +149,14 @@

    Summarize "count within" distances

    summary calculation.

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

    Arguments

    diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index c8c51df..32cbd75 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -165,15 +165,16 @@

    Value

    A table containing percent values as decimal fractions.

    See also

    -

    Other aggregation functions: compute_density_from_cell_summary, - compute_density_from_table, - compute_h_score_from_score_data, - compute_h_score, - compute_mean_expression_many, - compute_mean_expression, - compute_positivity_many, - compute_positivity, - count_phenotypes

    +

    Other aggregation functions: +compute_density_from_cell_summary(), +compute_density_from_table(), +compute_h_score_from_score_data(), +compute_h_score(), +compute_mean_expression_many(), +compute_mean_expression(), +compute_positivity_many(), +compute_positivity(), +count_phenotypes()

    diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index 1225b15..aab1be5 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -147,8 +147,7 @@

    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

    diff --git a/docs/reference/nearest_neighbor_map.html b/docs/reference/nearest_neighbor_map.html index 5a8b612..d46e924 100644 --- a/docs/reference/nearest_neighbor_map.html +++ b/docs/reference/nearest_neighbor_map.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -145,9 +145,17 @@

    Make a nearest neighbor map for a single field

    shown with any available phenotype.

    - 
    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)
    + 
    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
+)

    Arguments

    diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html index d2432f4..1cb8b99 100644 --- a/docs/reference/nearest_neighbor_summary.html +++ b/docs/reference/nearest_neighbor_summary.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -145,8 +145,12 @@

    Summarize nearest neighbor distances

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

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

    Arguments

    diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index e9d8535..78cb728 100644 --- a/docs/reference/order_by_slide_and_tissue_category.html +++ b/docs/reference/order_by_slide_and_tissue_category.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -153,8 +153,7 @@

    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

    diff --git a/docs/reference/spatial_map_viewer.html b/docs/reference/spatial_map_viewer.html index 6352ac3..894bcd7 100644 --- a/docs/reference/spatial_map_viewer.html +++ b/docs/reference/spatial_map_viewer.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index cb19cc0..a821a82 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index 61bbdb2..319bb06 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index f373934..0a469ab 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -69,7 +69,7 @@ phenoptrReports - 0.2.5 + 0.2.6 diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html index a5d6e6a..0688764 100644 --- a/docs/reference/write_count_within_sheet.html +++ b/docs/reference/write_count_within_sheet.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -145,8 +145,12 @@

    Write a "count within" summary to an Excel workbook

    sheet in an Excel workbook.

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

    Arguments

    @@ -171,14 +175,15 @@

    Arg

    See also

    -

    Other output functions: write_counts_sheet, - write_density_sheet, - write_expression_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_counts_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -143,8 +143,12 @@

    Write a cell counts table to an Excel workbook

    Write a formatted cell counts table to a sheet in an Excel workbook.

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

    Arguments

    @@ -170,14 +174,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_density_sheet, - write_expression_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -143,8 +143,12 @@

    Write a density table to an Excel workbook

    Write a formatted density table to a sheet in an Excel workbook.

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

    Arguments

    @@ -171,14 +175,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_expression_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -143,8 +143,12 @@

    Write an expression table to an Excel workbook

    Write a formatted cell expression table to a sheet in an Excel workbook.

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

    Arguments

    @@ -171,14 +175,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_density_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_density_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -143,8 +143,13 @@

    Write an H-Score table to an Excel workbook

    Write a formatted H-Score table to a sheet in an Excel workbook.

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

    Arguments

    @@ -166,19 +171,25 @@

    Arg

    + + + +
    sheet_title

    Optional title header for the table. If omitted, the title will be inferred from the h_score data if possible.

    marker

    Optional marker name to add to the default sheet title. +Ignored if sheet_title is provided.

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_density_sheet, - write_expression_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -145,9 +145,12 @@

    Write a nearest neighbor summary to an Excel workbook

    sheet in an Excel workbook.

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

    Arguments

    @@ -172,14 +175,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_density_sheet, - write_expression_sheet, - write_h_score_sheet, - write_percents_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_percents_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -143,8 +143,12 @@

    Write a cell percent table to an Excel workbook

    Write a formatted cell percent table to a sheet in an Excel workbook.

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

    Arguments

    @@ -170,14 +174,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_density_sheet, - write_expression_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_plot_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_plot_sheet(), +write_summary_sheet()

    @@ -143,8 +143,12 @@

    Write a plot to an Excel workbook

    Write a plot to a sheet in an Excel workbook.

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

    Arguments

    @@ -169,14 +173,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_density_sheet, - write_expression_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_summary_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_summary_sheet()

    diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index d44e6ff..730c053 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -77,7 +77,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -159,8 +159,15 @@

    Write a single sheet with formatting common to all sheets.

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

    Arguments

    diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index 3069f97..e46eb22 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -147,8 +147,13 @@

    Create summary charts from the results of an analysis

    of output_path, which must be either .docx or .html.

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

    Arguments

    diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index ec31c0b..fdb375f 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -145,8 +145,12 @@

    Create a summary report for a cell seg data file

    in a single cell seg data file.

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

    Arguments

    diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index 0e1510e..316cea6 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -70,7 +70,7 @@ phenoptrReports - 0.2.5 + 0.2.6 @@ -166,14 +166,15 @@

    Arg

    See also

    -

    Other output functions: write_count_within_sheet, - write_counts_sheet, - write_density_sheet, - write_expression_sheet, - write_h_score_sheet, - write_nearest_neighbor_summary_sheet, - write_percents_sheet, - write_plot_sheet

    +

    Other output functions: +write_count_within_sheet(), +write_counts_sheet(), +write_density_sheet(), +write_expression_sheet(), +write_h_score_sheet(), +write_nearest_neighbor_summary_sheet(), +write_percents_sheet(), +write_plot_sheet()