diff --git a/DESCRIPTION b/DESCRIPTION index baf0da7..439ba01 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.2.9.1 -Date: 2020-08-22 +Version: 0.2.10 +Date: 2020-11-11 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), diff --git a/NEWS.md b/NEWS.md index cf4b2af..4c7d5be 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,15 @@ +# phenoptrReports 0.2.10 +**2020-11-11** + +Consolidate and summarize addin: +- Reduce memory use to allow consolidation of larger files + +Bug fixes: +- Nearest neighbor and count within summaries work correctly + if detailed data is not requested. +- Correctly double-escape *all* backslashes in the slide id prefix. +- Improved error checks and error messages + # phenoptrReports 0.2.9 **2020-08-22** diff --git a/docs/404.html b/docs/404.html index 43b4782..c6c59e8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f5077b9..f601703 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index 0ba523d..a1417ad 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.9 + 0.2.10 @@ -93,13 +93,13 @@ -
+

Analyzing inForm data

Kent Johnson

-

2020-09-22

+

2020-11-11

Source: vignettes/analysis.Rmd diff --git a/docs/articles/analysis_files/header-attrs-2.3/header-attrs.js b/docs/articles/analysis_files/header-attrs-2.3/header-attrs.js new file mode 100644 index 0000000..dd57d92 --- /dev/null +++ b/docs/articles/analysis_files/header-attrs-2.3/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index 9c35c01..26df029 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.9 + 0.2.10
@@ -93,13 +93,13 @@ -
+

Consolidating inForm data

Kent Johnson

-

2020-09-22

+

2020-11-11

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/consolidation_files/header-attrs-2.3/header-attrs.js b/docs/articles/consolidation_files/header-attrs-2.3/header-attrs.js new file mode 100644 index 0000000..dd57d92 --- /dev/null +++ b/docs/articles/consolidation_files/header-attrs-2.3/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/index.html b/docs/articles/index.html index c7757ed..6ff1ccb 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/articles/spatial_map_viewer.html b/docs/articles/spatial_map_viewer.html index 20e5d96..e1b9e0c 100644 --- a/docs/articles/spatial_map_viewer.html +++ b/docs/articles/spatial_map_viewer.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.9 + 0.2.10
@@ -93,13 +93,13 @@ -
+

Viewing nearest neighbors

Kent Johnson

-

2020-09-22

+

2020-11-11

Source: vignettes/spatial_map_viewer.Rmd diff --git a/docs/articles/spatial_map_viewer_files/header-attrs-2.3/header-attrs.js b/docs/articles/spatial_map_viewer_files/header-attrs-2.3/header-attrs.js new file mode 100644 index 0000000..dd57d92 --- /dev/null +++ b/docs/articles/spatial_map_viewer_files/header-attrs-2.3/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/unmixing_quality_report.html b/docs/articles/unmixing_quality_report.html index ac53d2d..bdd1203 100644 --- a/docs/articles/unmixing_quality_report.html +++ b/docs/articles/unmixing_quality_report.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.9 + 0.2.10
@@ -93,13 +93,13 @@ -
+

Unmixing quality report

Kent Johnson

-

2020-09-22

+

2020-11-11

Source: vignettes/unmixing_quality_report.Rmd diff --git a/docs/articles/unmixing_quality_report_files/header-attrs-2.3/header-attrs.js b/docs/articles/unmixing_quality_report_files/header-attrs-2.3/header-attrs.js new file mode 100644 index 0000000..dd57d92 --- /dev/null +++ b/docs/articles/unmixing_quality_report_files/header-attrs-2.3/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/authors.html b/docs/authors.html index 3431948..4254bb8 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/index.html b/docs/index.html index 7ffbd98..1acbfe0 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/news/index.html b/docs/news/index.html index c638f74..b61cd54 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.9 + 0.2.10
@@ -140,6 +140,21 @@

Changelog

Source: NEWS.md
+
+

+phenoptrReports 0.2.10

+

2020-11-11

+

Consolidate and summarize addin:

+
    +
  • Reduce memory use to allow consolidation of larger files
    • +
+

Bug fixes:

+
    +
  • Nearest neighbor and count within summaries work correctly if detailed data is not requested.
    • +
  • Correctly double-escape all backslashes in the slide id prefix.
    • +
  • Improved error checks and error messages
    • +
+

phenoptrReports 0.2.9

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 1dd0974..4cd61e3 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.7.3 +pandoc: 2.9.2.1 pkgdown: 1.6.1 pkgdown_sha: ~ articles: @@ -6,7 +6,7 @@ articles: consolidation: consolidation.html spatial_map_viewer: spatial_map_viewer.html unmixing_quality_report: unmixing_quality_report.html -last_built: 2020-09-22T19:27Z +last_built: 2020-11-11T20:35Z 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 39f93ce..ad2bea5 100644 --- a/docs/reference/addin_10_merge.html +++ b/docs/reference/addin_10_merge.html @@ -77,7 +77,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html index 9ca6a88..28e398b 100644 --- a/docs/reference/addin_20_consolidate.html +++ b/docs/reference/addin_20_consolidate.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html index d37e21c..5445d94 100644 --- a/docs/reference/addin_30_analysis_app.html +++ b/docs/reference/addin_30_analysis_app.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/addin_35_spatial_map_viewer.html b/docs/reference/addin_35_spatial_map_viewer.html index 9685f75..f54b665 100644 --- a/docs/reference/addin_35_spatial_map_viewer.html +++ b/docs/reference/addin_35_spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html index 48876d4..8fe48d6 100644 --- a/docs/reference/addin_40_unmixing_quality.html +++ b/docs/reference/addin_40_unmixing_quality.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html index 9474717..82659cb 100644 --- a/docs/reference/addin_50_component_levels.html +++ b/docs/reference/addin_50_component_levels.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/choose_directory.html b/docs/reference/choose_directory.html index c68f131..0348f10 100644 --- a/docs/reference/choose_directory.html +++ b/docs/reference/choose_directory.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/choose_files.html b/docs/reference/choose_files.html index 8b5ac82..8fb80c8 100644 --- a/docs/reference/choose_files.html +++ b/docs/reference/choose_files.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/component_levels_report.html b/docs/reference/component_levels_report.html index 02223e0..c1df8ef 100644 --- a/docs/reference/component_levels_report.html +++ b/docs/reference/component_levels_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10
diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index c8dc4eb..67ea53f 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index a93a853..c13e323 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index a483499..2e686ed 100644 --- a/docs/reference/compute_h_score.html +++ b/docs/reference/compute_h_score.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index 564ae30..eb76b42 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 - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index d0dcbb2..bc0bafd 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index 4d6ce22..8bd1523 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 2194882..379bc5d 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index 08df90e..bbe7421 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/consolidate_and_summarize_cell_seg_data.html b/docs/reference/consolidate_and_summarize_cell_seg_data.html index 3d4d957..9bef197 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 - 0.2.9 + 0.2.10 diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index 633cc9b..b387383 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/count_within_summary.html b/docs/reference/count_within_summary.html index 1b6534b..c7da2db 100644 --- a/docs/reference/count_within_summary.html +++ b/docs/reference/count_within_summary.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index 0663eb5..37f4c8e 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/index.html b/docs/reference/index.html index cad7f92..6dab2f9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/merge_cell_seg_files.html b/docs/reference/merge_cell_seg_files.html index b92d185..87cd6d1 100644 --- a/docs/reference/merge_cell_seg_files.html +++ b/docs/reference/merge_cell_seg_files.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/nearest_neighbor_map.html b/docs/reference/nearest_neighbor_map.html index 12abfa2..ad2937d 100644 --- a/docs/reference/nearest_neighbor_map.html +++ b/docs/reference/nearest_neighbor_map.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/nearest_neighbor_summary.html b/docs/reference/nearest_neighbor_summary.html index 48f076a..289f885 100644 --- a/docs/reference/nearest_neighbor_summary.html +++ b/docs/reference/nearest_neighbor_summary.html @@ -79,7 +79,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index bd42898..e99c98a 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 - 0.2.9 + 0.2.10 diff --git a/docs/reference/spatial_map_viewer.html b/docs/reference/spatial_map_viewer.html index bb00c40..5c7d832 100644 --- a/docs/reference/spatial_map_viewer.html +++ b/docs/reference/spatial_map_viewer.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index deb5eb3..193c368 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/unmixing_quality_report.html b/docs/reference/unmixing_quality_report.html index 46c06e5..bfed8ed 100644 --- a/docs/reference/unmixing_quality_report.html +++ b/docs/reference/unmixing_quality_report.html @@ -75,7 +75,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index d67a78b..5d1b2aa 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_count_within_sheet.html b/docs/reference/write_count_within_sheet.html index 994abc7..f2fd102 100644 --- a/docs/reference/write_count_within_sheet.html +++ b/docs/reference/write_count_within_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index 05c606d..c74c9bf 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index 0850c31..f113c0f 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index ce30ee3..7d28e6a 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index 555f6f1..3ce2739 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_nearest_neighbor_summary_sheet.html b/docs/reference/write_nearest_neighbor_summary_sheet.html index 6eea7d4..f756c7e 100644 --- a/docs/reference/write_nearest_neighbor_summary_sheet.html +++ b/docs/reference/write_nearest_neighbor_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index 5b5acb8..a1eb29d 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index 5bd1777..ce55443 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -72,7 +72,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_session_info.html b/docs/reference/write_session_info.html index 8e93cdd..6d4e1e2 100644 --- a/docs/reference/write_session_info.html +++ b/docs/reference/write_session_info.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index f80b89e..70fc6f9 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -80,7 +80,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index 0f3dd4e..1dea010 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -74,7 +74,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index 3700bf3..d792155 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10 diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index 7e02cc8..28df08b 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -73,7 +73,7 @@ phenoptrReports - 0.2.9 + 0.2.10