From 0a9d2c81a119cbbeaef3cfcc413f6b72b99c4d93 Mon Sep 17 00:00:00 2001 From: Kent Johnson Date: Mon, 18 May 2020 14:15:13 -0400 Subject: [PATCH] Bump to version 0.2.8 and rebuild docs --- DESCRIPTION | 4 ++-- NEWS.md | 3 ++- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/analysis.html | 4 ++-- docs/articles/consolidation.html | 4 ++-- docs/articles/index.html | 2 +- docs/articles/spatial_map_viewer.html | 6 +++--- docs/articles/unmixing_quality_report.html | 4 ++-- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 19 ++++++++++++++++++- docs/pkgdown.yml | 2 +- docs/reference/addin_10_merge.html | 2 +- docs/reference/addin_20_consolidate.html | 2 +- docs/reference/addin_30_analysis_app.html | 2 +- .../addin_35_spatial_map_viewer.html | 2 +- docs/reference/addin_40_unmixing_quality.html | 2 +- docs/reference/addin_50_component_levels.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 | 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 | 2 +- docs/reference/count_phenotypes.html | 2 +- docs/reference/count_within_summary.html | 2 +- docs/reference/counts_to_percents.html | 2 +- docs/reference/index.html | 2 +- docs/reference/merge_cell_seg_files.html | 2 +- docs/reference/nearest_neighbor_map.html | 2 +- docs/reference/nearest_neighbor_summary.html | 2 +- .../order_by_slide_and_tissue_category.html | 2 +- docs/reference/spatial_map_viewer.html | 2 +- docs/reference/split_phenotypes.html | 2 +- docs/reference/unmixing_quality_report.html | 2 +- docs/reference/upset_plot.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 | 2 +- docs/reference/write_summary_report.html | 2 +- docs/reference/write_summary_sheet.html | 2 +- 56 files changed, 80 insertions(+), 62 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e7868ec..31ea79e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.2.7.9000 -Date: 2020-04-23 +Version: 0.2.8 +Date: 2020-05-18 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), diff --git a/NEWS.md b/NEWS.md index ac631ea..0bad5a5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# phenoptrReports 0.2.7.9000 +# phenoptrReports 0.2.8 +**2020-05-18** Analysis addin: - Remove summary lines from the Count Within worksheet, they are not diff --git a/docs/404.html b/docs/404.html index 049161b..9b94a68 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index ef4a1f0..fc0d24a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index d0f300b..bb87064 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.7 + 0.2.8 @@ -99,7 +99,7 @@

Analyzing inForm data

Kent Johnson

-

2020-04-23

+

2020-05-18

Source: vignettes/analysis.Rmd diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index 3ea31a8..60af556 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.7 + 0.2.8 @@ -99,7 +99,7 @@

Consolidating inForm data

Kent Johnson

-

2020-04-23

+

2020-05-18

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 85a0763..50c07b2 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/articles/spatial_map_viewer.html b/docs/articles/spatial_map_viewer.html index c9e0498..87a0ccb 100644 --- a/docs/articles/spatial_map_viewer.html +++ b/docs/articles/spatial_map_viewer.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.7 + 0.2.8 @@ -99,7 +99,7 @@

Viewing nearest neighbors

Kent Johnson

-

2020-04-23

+

2020-05-18

Source: vignettes/spatial_map_viewer.Rmd @@ -163,7 +163,7 @@

  • Select the type of nearest neighbor relationship “Nearest neighbor” is not a symmetric relationship—cell A may have a nearest neighbor B, whose nearest neighbor is not A. Try the different settings to find the one you want.

  • Control the dot size This slider controls the size of the dots displaying the cells. You may want to make the dots smaller before saving images.

  • -

    Save a single view or views for all fields The “Save image” button will save the currently displayed image in your browser’s Download folder. The “Save all” button will use the current settings to save a zip file containing images of all fields in the experiment.

    +

    Save a single view or views for all fields The “Save image” button will save the currently displayed image in your browser’s Download folder. The “Save all” button will use the current settings to save a directory or zip file containing images of all fields in the experiment.

    • Select “Save data with image” to save a tab-separated data file with the image(s).
    • Select “Show logo” to include the Akoya Biosciences logo in the image(s). Deselect to show or save images without the logo.
      • diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index e3c7691..7404199 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.7 + 0.2.8 @@ -99,7 +99,7 @@

      Unmixing quality report

      Kent Johnson

      -

      2020-04-23

      +

      2020-05-18

      Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/authors.html b/docs/authors.html index 174dc0b..2e5aef7 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/index.html b/docs/index.html index edb14e7..942a04d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/news/index.html b/docs/news/index.html index 8c4553e..ca16322 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.7 + 0.2.8 @@ -140,6 +140,23 @@

      Changelog

      Source: NEWS.md +
      +

      +phenoptrReports 0.2.8

      +

      2020-05-18

      +

      Analysis addin:

      +
        +
      • Remove summary lines from the Count Within worksheet, they are not correct (#35)!
        • +
      +

      Spatial map viewer addin:

      +
        +
      • For the usual use where the client browser is running on the user’s computer, the “Save all” saves directly to the local file system without creating an intermediate zip file. This is faster and avoids transfer of a potentially large zip file.
        • +
      +

      Misc:

      +
        +
      • Fix to work correctly with dplyr 1.0.0.
        • +
      +

      phenoptrReports 0.2.7

      diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 23d6ca5..3bf0c00 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: 2020-04-23T18:55Z +last_built: 2020-05-18T18:01Z 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 f073908..2b7b44b 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -77,7 +77,7 @@ phenoptrReports - 0.2.7 + 0.2.8
      diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index d150c03..0cc896c 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index d6b2e0b..db2aa00 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/addin_35_spatial_map_viewer.html b/docs/reference/addin_35_spatial_map_viewer.html index e3b5e5b..b1d74c7 100644 --- a/docs/reference/addin_35_spatial_map_viewer.html +++ b/docs/reference/addin_35_spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index 7914fec..f27caa5 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index a26d25e..15c6e2c 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html index 39d5953..42db9d1 100644 --- a/docs/reference/choose_directory.html +++ b/docs/reference/choose_directory.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html index c3bf137..9b97f07 100644 --- a/docs/reference/choose_files.html +++ b/docs/reference/choose_files.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index 2c0f8ea..a19375a 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 4e56e2a..911a5c8 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index 6ae48fd..bb3004f 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index e734223..05ccedb 100644 --- a/docs/reference/compute_h_score.html +++ b/docs/reference/compute_h_score.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index 1306df1..dc08437 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 - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index f95c0fe..36450b2 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index 66bdf6c..e317576 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 39802ab..9b66bfa 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index 542c30a..2c450fa 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/consolidate_and_summarize_cell_seg_data.html b/docs/reference/consolidate_and_summarize_cell_seg_data.html index a6d6b53..b056bde 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 - 0.2.7 + 0.2.8 diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index d380031..5f2d905 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/count_within_summary.html b/docs/reference/count_within_summary.html index f1abb9d..a65717a 100644 --- a/docs/reference/count_within_summary.html +++ b/docs/reference/count_within_summary.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index 81a7540..e67b01f 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/index.html b/docs/reference/index.html index 87436e7..17556f3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index 8725bea..f1c257d 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/nearest_neighbor_map.html b/docs/reference/nearest_neighbor_map.html index 56a6087..ffcb2f1 100644 --- a/docs/reference/nearest_neighbor_map.html +++ b/docs/reference/nearest_neighbor_map.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html index ba04240..3f21af5 100644 --- a/docs/reference/nearest_neighbor_summary.html +++ b/docs/reference/nearest_neighbor_summary.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index cd9a1bf..abcdf1c 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 - 0.2.7 + 0.2.8 diff --git a/docs/reference/spatial_map_viewer.html b/docs/reference/spatial_map_viewer.html index 0dcdc67..e546233 100644 --- a/docs/reference/spatial_map_viewer.html +++ b/docs/reference/spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index 1404fd4..5735ccd 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index 8b61b20..6df9a8c 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index 0f96cab..c835e92 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html index 083f3ce..6ebf1d9 100644 --- a/docs/reference/write_count_within_sheet.html +++ b/docs/reference/write_count_within_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index 53b6ece..68d9124 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index bfc2776..06ddb04 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index 75e2713..06eea12 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index fa31226..f0833a5 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_nearest_neighbor_summary_sheet.html b/docs/reference/write_nearest_neighbor_summary_sheet.html index 621cb2f..38edf25 100644 --- a/docs/reference/write_nearest_neighbor_summary_sheet.html +++ b/docs/reference/write_nearest_neighbor_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index 8039e4d..26535ff 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index 2ea7bc5..122a852 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_session_info.html b/docs/reference/write_session_info.html index 9943433..878be83 100644 --- a/docs/reference/write_session_info.html +++ b/docs/reference/write_session_info.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index 5655d1c..4dd54cc 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -80,7 +80,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index c647188..e66e3c7 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index fb307a2..57dc73c 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8 diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index e71eb3a..b3e0b0b 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.7 + 0.2.8