From 529e16e56b4dffb60e0fc45c4f2e172dedb02e9c Mon Sep 17 00:00:00 2001 From: Kent Johnson Date: Wed, 18 Aug 2021 13:48:18 -0400 Subject: [PATCH] Prep for release: bump version, rebuild docs, cleanup --- DESCRIPTION | 4 +- NEWS.md | 11 +- _pkgdown.yml | 7 +- docs/404.html | 16 +- docs/LICENSE-text.html | 16 +- docs/articles/analysis.html | 20 +- .../header-attrs-2.9/header-attrs.js | 12 + docs/articles/component_levels_report.html | 12 +- docs/articles/consolidation.html | 20 +- .../header-attrs-2.9/header-attrs.js | 12 + docs/articles/index.html | 22 +- docs/articles/spatial_map_viewer.html | 20 +- .../header-attrs-2.9/header-attrs.js | 12 + .../articles/staining_consistency_report.html | 14 +- docs/articles/top_20_bottom_10_report.html | 12 +- docs/articles/unmixing_quality_report.html | 20 +- .../header-attrs-2.9/header-attrs.js | 12 + docs/authors.html | 18 +- docs/index.html | 32 ++- docs/news/index.html | 51 +++- docs/pkgdown.yml | 5 +- docs/reference/addin_10_merge.html | 16 +- docs/reference/addin_20_consolidate.html | 16 +- docs/reference/addin_30_analysis_app.html | 16 +- .../addin_35_spatial_map_viewer.html | 16 +- docs/reference/addin_40_unmixing_quality.html | 16 +- docs/reference/addin_50_component_levels.html | 16 +- ...addin_60_mean_of_top_and_bottom_cells.html | 195 ++++++++++++++ .../addin_70_staining_consistency_report.html | 193 ++++++++++++++ docs/reference/choose_directory.html | 16 +- docs/reference/choose_files.html | 16 +- docs/reference/component_levels_report.html | 16 +- .../compute_density_from_cell_summary.html | 16 +- .../reference/compute_density_from_table.html | 16 +- docs/reference/compute_h_score.html | 16 +- .../compute_h_score_from_score_data.html | 16 +- docs/reference/compute_mean_expression.html | 16 +- .../compute_mean_expression_many.html | 16 +- docs/reference/compute_positivity.html | 16 +- docs/reference/compute_positivity_many.html | 16 +- ...nsolidate_and_summarize_cell_seg_data.html | 16 +- docs/reference/count_phenotypes.html | 16 +- docs/reference/count_within_summary.html | 16 +- docs/reference/counts_to_percents.html | 16 +- docs/reference/discrete_colors.html | 16 +- docs/reference/index.html | 76 +++++- .../mean_of_top_and_bottom_cells.html | 242 ++++++++++++++++++ .../mean_of_top_and_bottom_cells_report.html | 220 ++++++++++++++++ docs/reference/merge_cell_seg_files.html | 16 +- docs/reference/nearest_neighbor_map.html | 21 +- docs/reference/nearest_neighbor_summary.html | 16 +- .../order_by_slide_and_tissue_category.html | 16 +- docs/reference/spatial_map_viewer.html | 16 +- docs/reference/split_phenotype_column.html | 16 +- docs/reference/split_phenotypes.html | 16 +- .../staining_consistency_report.html | 210 +++++++++++++++ docs/reference/unmixing_quality_report.html | 16 +- docs/reference/upset_plot.html | 16 +- docs/reference/write_count_within_sheet.html | 16 +- docs/reference/write_counts_sheet.html | 16 +- docs/reference/write_density_sheet.html | 16 +- docs/reference/write_expression_sheet.html | 16 +- docs/reference/write_h_score_sheet.html | 18 +- .../write_mean_of_top_and_bottom_charts.html | 215 ++++++++++++++++ .../write_nearest_neighbor_summary_sheet.html | 16 +- docs/reference/write_percents_sheet.html | 16 +- docs/reference/write_plot_sheet.html | 16 +- docs/reference/write_session_info.html | 16 +- docs/reference/write_sheet.html | 16 +- docs/reference/write_summary_charts.html | 16 +- docs/reference/write_summary_report.html | 16 +- docs/reference/write_summary_sheet.html | 16 +- docs/sitemap.xml | 27 ++ inst/WORDLIST | 7 + vignettes/staining_consistency_report.Rmd | 4 +- 75 files changed, 2137 insertions(+), 311 deletions(-) create mode 100644 docs/articles/analysis_files/header-attrs-2.9/header-attrs.js create mode 100644 docs/articles/consolidation_files/header-attrs-2.9/header-attrs.js create mode 100644 docs/articles/spatial_map_viewer_files/header-attrs-2.9/header-attrs.js create mode 100644 docs/articles/unmixing_quality_report_files/header-attrs-2.9/header-attrs.js create mode 100644 docs/reference/addin_60_mean_of_top_and_bottom_cells.html create mode 100644 docs/reference/addin_70_staining_consistency_report.html create mode 100644 docs/reference/mean_of_top_and_bottom_cells.html create mode 100644 docs/reference/mean_of_top_and_bottom_cells_report.html create mode 100644 docs/reference/staining_consistency_report.html create mode 100644 docs/reference/write_mean_of_top_and_bottom_charts.html diff --git a/DESCRIPTION b/DESCRIPTION index 0f08467..6b0d184 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.2.13.9000 -Date: 2021-06-10 +Version: 0.3.0 +Date: 2021-08-18 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), diff --git a/NEWS.md b/NEWS.md index 351b577..6974ba9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,5 @@ -# phenoptrReports 0.2.13.9000 - -Staining consistency report: -- New addin creates a report showing mean expression of a selected marker - across multiple samples. +# phenoptrReports 0.3.0 +**2021-08-18** Mean of top 20 / bottom 10 addin: - New addin helps to evaluate whether the staining quality is @@ -10,6 +7,10 @@ Mean of top 20 / bottom 10 addin: https://akoyabio.github.io/phenoptrReports/articles/top_20_bottom_10_report.html for details. +Staining consistency report: +- New addin creates a report showing mean expression of a selected marker + across multiple samples. + Analysis addin: - Fix problem computing mean expression for phenotypes with formulas in their definition #47 diff --git a/_pkgdown.yml b/_pkgdown.yml index 8bb6f42..eea5d0e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -20,6 +20,10 @@ navbar: href: articles/spatial_map_viewer.html - text: "Unmixing quality report" href: articles/unmixing_quality_report.html + - text: "Mean of top 20 / bottom 10 cells report" + href: articles/top_20_bottom_10_report.html + - text: "Staining consistency report" + href: articles/staining_consistency_report.html - text: "Reference" href: reference/index.html right: @@ -83,8 +87,9 @@ reference: - title: Data reporting - HTML desc: These functions write analysis results to HTML reports. contents: - - unmixing_quality_report - component_levels_report + - staining_consistency_report + - unmixing_quality_report - write_summary_report - title: Data reporting - Excel and Word desc: These functions write analysis results to Excel worksheets diff --git a/docs/404.html b/docs/404.html index fcc0a78..4004561 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.13 + 0.3.0 @@ -79,7 +79,7 @@
  • @@ -111,14 +117,14 @@