diff --git a/docs/404.html b/docs/404.html index 66a0191..69af5be 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index e1f0efe..821f484 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index f96c707..0570ab8 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -99,7 +99,7 @@

Analyzing inForm data

Kent Johnson

-

2021-06-01

+

2021-06-10

Source: vignettes/analysis.Rmd diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index f50b7cd..346159e 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -99,7 +99,7 @@

Consolidating inForm data

Kent Johnson

-

2021-06-01

+

2021-06-10

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 2acff57..9f7bb99 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/articles/spatial_map_viewer.html b/docs/articles/spatial_map_viewer.html index c94963a..17b300e 100644 --- a/docs/articles/spatial_map_viewer.html +++ b/docs/articles/spatial_map_viewer.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -99,7 +99,7 @@

Viewing nearest neighbors

Kent Johnson

-

2021-06-01

+

2021-06-10

Source: vignettes/spatial_map_viewer.Rmd diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index 9e8c88e..4e9dcb4 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -99,7 +99,7 @@

Unmixing quality report

Kent Johnson

-

2021-06-01

+

2021-06-10

Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/authors.html b/docs/authors.html index edbad2d..59f0a0e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/index.html b/docs/index.html index 9db89d9..a249b4e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/news/index.html b/docs/news/index.html index fd50413..ef96425 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -140,6 +140,14 @@

Changelog

Source: NEWS.md +
+

+phenoptrReports 0.2.12

+

2021-06-10

+ +

phenoptrReports 0.2.11

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 540f35f..08886c4 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,7 +6,7 @@ articles: consolidation: consolidation.html spatial_map_viewer: spatial_map_viewer.html unmixing_quality_report: unmixing_quality_report.html -last_built: 2021-06-01T15:18Z +last_built: 2021-06-10T14:09Z urls: reference: http://akoyabio.github.io/phenoptrReports/reference article: http://akoyabio.github.io/phenoptrReports/articles diff --git a/docs/reference/addin_10_merge.html b/docs/reference/addin_10_merge.html index be2987f..79ffa6c 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -77,7 +77,7 @@ phenoptrReports - 0.2.11 + 0.2.12
diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index acc79b9..93ba7a4 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index 6cea0f3..5acd9fb 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/addin_35_spatial_map_viewer.html b/docs/reference/addin_35_spatial_map_viewer.html index aa93c79..5d46a15 100644 --- a/docs/reference/addin_35_spatial_map_viewer.html +++ b/docs/reference/addin_35_spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index 66efb19..616257c 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index 67186c0..a793f2b 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html index d1f6426..2e59b7a 100644 --- a/docs/reference/choose_directory.html +++ b/docs/reference/choose_directory.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html index 16888bf..aa9bedc 100644 --- a/docs/reference/choose_files.html +++ b/docs/reference/choose_files.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index 8fc43f9..2798305 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 6b418d0..0576df2 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index 051c16b..b81513c 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index fda02be..5a5f220 100644 --- a/docs/reference/compute_h_score.html +++ b/docs/reference/compute_h_score.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index c8d95bd..6c42518 100644 --- a/docs/reference/compute_h_score_from_score_data.html +++ b/docs/reference/compute_h_score_from_score_data.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index 1cf39f0..8375505 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index b19bd02..186245b 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 0bbabdb..2d0bb0b 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index 8da6e23..72c6ef2 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/consolidate_and_summarize_cell_seg_data.html b/docs/reference/consolidate_and_summarize_cell_seg_data.html index 9ddf434..c47c631 100644 --- a/docs/reference/consolidate_and_summarize_cell_seg_data.html +++ b/docs/reference/consolidate_and_summarize_cell_seg_data.html @@ -76,7 +76,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index bfd37df..a52244d 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/count_within_summary.html b/docs/reference/count_within_summary.html index f2d28df..e7bb971 100644 --- a/docs/reference/count_within_summary.html +++ b/docs/reference/count_within_summary.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index 81e283a..70fa8b1 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/discrete_colors.html b/docs/reference/discrete_colors.html index 3690827..e01e8ac 100644 --- a/docs/reference/discrete_colors.html +++ b/docs/reference/discrete_colors.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/index.html b/docs/reference/index.html index 13a6c4a..69fddb5 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -473,7 +473,7 @@

split_phenotypes()

-

Split a phenotype column

+

Split all phenotype columns

diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index 5321a12..3c65537 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/nearest_neighbor_map.html b/docs/reference/nearest_neighbor_map.html index e382efb..bfbfc2a 100644 --- a/docs/reference/nearest_neighbor_map.html +++ b/docs/reference/nearest_neighbor_map.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html index c39c312..4f071e4 100644 --- a/docs/reference/nearest_neighbor_summary.html +++ b/docs/reference/nearest_neighbor_summary.html @@ -79,7 +79,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index dd8c1cd..280eec0 100644 --- a/docs/reference/order_by_slide_and_tissue_category.html +++ b/docs/reference/order_by_slide_and_tissue_category.html @@ -78,7 +78,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/spatial_map_viewer.html b/docs/reference/spatial_map_viewer.html index d2d9d54..3ee7b34 100644 --- a/docs/reference/spatial_map_viewer.html +++ b/docs/reference/spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/split_phenotype_column.html b/docs/reference/split_phenotype_column.html new file mode 100644 index 0000000..5429e6e --- /dev/null +++ b/docs/reference/split_phenotype_column.html @@ -0,0 +1,202 @@ + + + + + + + + +Split a single phenotype column — split_phenotype_column • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Split a single phenotype column

+ Source: R/split_phenotypes.R + +
+ +
+

A column containing multiple phenotypes is split +into multiple columns, one for each single phenotype.

+
+ + 
split_phenotype_column(csd, column)
+ +

Arguments

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

Cell seg data to use.

column

The name of the column to split

+ +

Value

+ +

A new data frame with the column column replaced with +individual columns per phenotype and the Confidence column(s) removed.

+

Details

+ +

Multiple phenotypes in the original column must be separated with "/". +The names of positive phenotypes must end in "+".

+ +
+ +
+ + +
+
+

Developed by Kent S Johnson.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index b3a1e08..9c8b3c2 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -6,7 +6,7 @@ -Split a phenotype column — split_phenotypes • phenoptrReports +Split all phenotype columns — split_phenotypes • phenoptrReports @@ -39,8 +39,8 @@ - - + @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 @@ -138,13 +138,13 @@
-

Split a phenotype column

+

Split all phenotype columns

Source: R/split_phenotypes.R
-

A column containing multiple phenotypes is split +

All columns containing multiple phenotypes are split into multiple columns, one for each single phenotype.

@@ -161,8 +161,9 @@

Arg

Value

-

A new data frame with the Phenotype column replaced with -individual columns per phenotype and the Confidence column removed.

+

A new data frame with Phenotype and Phenotype-<scheme> columns +replaced with +individual columns per phenotype and the Confidence column(s) removed.

Details

Multiple phenotypes in the original column must be separated with "/". diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index d304a8a..888ffdc 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.11 + 0.2.12

diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index 413b483..a0c4132 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12
diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html index 40004b6..ac82e63 100644 --- a/docs/reference/write_count_within_sheet.html +++ b/docs/reference/write_count_within_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index 8f0a2bb..fcb3491 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index bba50ad..2561a85 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index 3db87a6..23b22f6 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index 92a9d6d..a6337d2 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_nearest_neighbor_summary_sheet.html b/docs/reference/write_nearest_neighbor_summary_sheet.html index 7bce123..7c7a40f 100644 --- a/docs/reference/write_nearest_neighbor_summary_sheet.html +++ b/docs/reference/write_nearest_neighbor_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index 5ea6676..9cf6f72 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index 77c3a9d..7e749fe 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_session_info.html b/docs/reference/write_session_info.html index d406db2..2c29107 100644 --- a/docs/reference/write_session_info.html +++ b/docs/reference/write_session_info.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index 6be08ee..ac1c732 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -80,7 +80,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index bf1b556..653e5d4 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index 4647801..b451ec4 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index 2637907..adecffb 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.11 + 0.2.12 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 258f5b9..3f2ab54 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -87,6 +87,9 @@ http://akoyabio.github.io/phenoptrReports/reference/split_phenotypes.html + + http://akoyabio.github.io/phenoptrReports/reference/split_phenotype_column.html + http://akoyabio.github.io/phenoptrReports/reference/unmixing_quality_report.html