diff --git a/DESCRIPTION b/DESCRIPTION index 0561526..d54a90a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.1.0 -Date: 2018-10-15 +Version: 0.1.1 +Date: 2018-10-22 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), email = "kjohnson@akoyabio.com"), diff --git a/NEWS.md b/NEWS.md index 505bf6e..a564336 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# phenoptrReports 0.1.0.9000 +# phenoptrReports 0.1.1.0 +**2018-10-22** New features: - Add version number, date stamp and doco link to generated script file #2 diff --git a/README.md b/README.md index fef4dcc..4499596 100644 --- a/README.md +++ b/README.md @@ -73,7 +73,7 @@ phenotype names should not end in "+". #### Merged cell seg data The primary source data for `phenoptrReports` is -one or more merged cell seg data files created in the inForm merge step. +one or more merged cell seg data files created in the inForm Review/Merge tab. You may use multiple merge files from multiple inForm projects with different phenotypes. The Slide ID and Cell ID fields in multiple merge files must agree exactly. diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 464da86..c4e1ce8 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index 2d7942f..63e9b88 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 @@ -92,7 +92,7 @@

Analyzing inForm data

Kent Johnson

-

2018-10-14

+

2018-10-22

Source: vignettes/analysis.Rmd diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index 81aa27b..a63154d 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 @@ -92,7 +92,7 @@

Consolidating inForm data

Kent Johnson

-

2018-10-14

+

2018-10-22

Source: vignettes/consolidation.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 56cf70c..915fbe6 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/authors.html b/docs/authors.html index 52c327d..f97dd58 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/favicon.ico b/docs/favicon.ico index 3f65034..19c6431 100644 Binary files a/docs/favicon.ico and b/docs/favicon.ico differ diff --git a/docs/index.html b/docs/index.html index d5c1a73..4772398 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 @@ -130,6 +130,32 @@

Getting Started

A phenoptrReports analysis has two major steps - data consolidation and data aggregation.

+
+

+Data requirements

+

phenoptrReports creates reports based on inForm output files.

+
+

+Tissue segmentation

+

inForm projects used with phenoptrReports must include a tissue segmentation step.

+
+
+

+Phenotypes

+

The names of positive phenotypes used with phenoptrReports must end with “+”, for example “CD8+” or “FoxP3+”. Negative and “Other” phenotype names should not end in “+”.

+
+
+

+Merged cell seg data

+

The primary source data for phenoptrReports is one or more merged cell seg data files created in the inForm Review/Merge tab. You may use multiple merge files from multiple inForm projects with different phenotypes. The Slide ID and Cell ID fields in multiple merge files must agree exactly.

+
+
+

+Other files

+

Two other input files are optional.

+

If provided, phenotprReports will use a merged cell seg summary file to compute tissue area and cell density within tissue categories. A score data summary file is used to compute H-Score per slide and tissue category.

+
+

Data consolidation

diff --git a/docs/news/index.html b/docs/news/index.html index 8dbe105..1df4c51 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1
@@ -124,6 +124,23 @@

Changelog

Source: NEWS.md +
+

+phenoptrReports 0.1.1.0

+

2018-10-22

+

New features:

+ +

Bug fixes:

+ +

phenoptrReports 0.1.0.0

@@ -138,6 +155,7 @@

Contents

diff --git a/docs/reference/add_tissue_category_totals.html b/docs/reference/add_tissue_category_totals.html index 6164f27..d461af6 100644 --- a/docs/reference/add_tissue_category_totals.html +++ b/docs/reference/add_tissue_category_totals.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1

diff --git a/docs/reference/analysis_app.html b/docs/reference/analysis_app.html index 32ac299..d648b0c 100644 --- a/docs/reference/analysis_app.html +++ b/docs/reference/analysis_app.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/check_phenotypes.html b/docs/reference/check_phenotypes.html index 807476f..28e3ed0 100644 --- a/docs/reference/check_phenotypes.html +++ b/docs/reference/check_phenotypes.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 9f90601..15937d3 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_density_from_table.html b/docs/reference/compute_density_from_table.html index b200811..ee4f28e 100644 --- a/docs/reference/compute_density_from_table.html +++ b/docs/reference/compute_density_from_table.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_h_score.html b/docs/reference/compute_h_score.html index 3817101..465035e 100644 --- a/docs/reference/compute_h_score.html +++ b/docs/reference/compute_h_score.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_h_score_from_score_data.html b/docs/reference/compute_h_score_from_score_data.html index cb6ffae..a46d897 100644 --- a/docs/reference/compute_h_score_from_score_data.html +++ b/docs/reference/compute_h_score_from_score_data.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_mean_expression.html b/docs/reference/compute_mean_expression.html index 2945397..8f2eac3 100644 --- a/docs/reference/compute_mean_expression.html +++ b/docs/reference/compute_mean_expression.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_mean_expression_many.html b/docs/reference/compute_mean_expression_many.html index 9e29c88..c8a2e07 100644 --- a/docs/reference/compute_mean_expression_many.html +++ b/docs/reference/compute_mean_expression_many.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_positivity.html b/docs/reference/compute_positivity.html index 07dbb03..68a5ddb 100644 --- a/docs/reference/compute_positivity.html +++ b/docs/reference/compute_positivity.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/compute_positivity_many.html b/docs/reference/compute_positivity_many.html index e56f369..c106196 100644 --- a/docs/reference/compute_positivity_many.html +++ b/docs/reference/compute_positivity_many.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/count_phenotypes.html b/docs/reference/count_phenotypes.html index 63cfcbf..0398d3b 100644 --- a/docs/reference/count_phenotypes.html +++ b/docs/reference/count_phenotypes.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/counts_to_percents.html b/docs/reference/counts_to_percents.html index c7ca9ea..48884ae 100644 --- a/docs/reference/counts_to_percents.html +++ b/docs/reference/counts_to_percents.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/field_column.html b/docs/reference/field_column.html new file mode 100644 index 0000000..d175450 --- /dev/null +++ b/docs/reference/field_column.html @@ -0,0 +1,186 @@ + + + + + + + + +Get the name of the column that distinguishes fields in a merged cell +seg data file. — field_column • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Get the name of the column that distinguishes fields in a merged cell +seg data file.

+ Source: R/utilities.R + +
+ +
+ +

Get the name of the column that distinguishes fields in a merged cell +seg data file.

+ +
+ + 
field_column(csd)
+ +

Arguments

+ + + + + + +
csd

Cell seg data

+ +

Value

+ +

A column name (as a string)

+ + +
+ +
+ + +
+ + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index a012f7f..4729221 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -61,7 +61,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/make_nested.html b/docs/reference/make_nested.html index 54a2b6d..df149e0 100644 --- a/docs/reference/make_nested.html +++ b/docs/reference/make_nested.html @@ -67,7 +67,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/make_unique_names.html b/docs/reference/make_unique_names.html index 11bc750..414b511 100644 --- a/docs/reference/make_unique_names.html +++ b/docs/reference/make_unique_names.html @@ -67,7 +67,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/merge_addin.html b/docs/reference/merge_addin.html index 5288017..7d3fb1b 100644 --- a/docs/reference/merge_addin.html +++ b/docs/reference/merge_addin.html @@ -67,7 +67,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/merge_and_split_cell_seg_data.html b/docs/reference/merge_and_split_cell_seg_data.html index 5d434b7..6161012 100644 --- a/docs/reference/merge_and_split_cell_seg_data.html +++ b/docs/reference/merge_and_split_cell_seg_data.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/merge_and_summarize_cell_seg_data.html b/docs/reference/merge_and_summarize_cell_seg_data.html index 421fe8d..e248c6d 100644 --- a/docs/reference/merge_and_summarize_cell_seg_data.html +++ b/docs/reference/merge_and_summarize_cell_seg_data.html @@ -68,7 +68,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/order_by_slide_and_tissue_category.html b/docs/reference/order_by_slide_and_tissue_category.html index 52f1536..25cf345 100644 --- a/docs/reference/order_by_slide_and_tissue_category.html +++ b/docs/reference/order_by_slide_and_tissue_category.html @@ -70,7 +70,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/split_phenotypes.html b/docs/reference/split_phenotypes.html index c519959..4acb0c6 100644 --- a/docs/reference/split_phenotypes.html +++ b/docs/reference/split_phenotypes.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/upset_data.html b/docs/reference/upset_data.html index 6e6b8b8..d305c71 100644 --- a/docs/reference/upset_data.html +++ b/docs/reference/upset_data.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/upset_plot.html b/docs/reference/upset_plot.html index aab79ad..c0572bb 100644 --- a/docs/reference/upset_plot.html +++ b/docs/reference/upset_plot.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index e0bda24..4f499f2 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_density_sheet.html b/docs/reference/write_density_sheet.html index c9d7e3a..808458b 100644 --- a/docs/reference/write_density_sheet.html +++ b/docs/reference/write_density_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_expression_sheet.html b/docs/reference/write_expression_sheet.html index dfe5940..fefe806 100644 --- a/docs/reference/write_expression_sheet.html +++ b/docs/reference/write_expression_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_h_score_sheet.html b/docs/reference/write_h_score_sheet.html index ba771ce..f32307c 100644 --- a/docs/reference/write_h_score_sheet.html +++ b/docs/reference/write_h_score_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_percents_sheet.html b/docs/reference/write_percents_sheet.html index 55129b6..94b7880 100644 --- a/docs/reference/write_percents_sheet.html +++ b/docs/reference/write_percents_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_plot_sheet.html b/docs/reference/write_plot_sheet.html index b41399b..daaedce 100644 --- a/docs/reference/write_plot_sheet.html +++ b/docs/reference/write_plot_sheet.html @@ -64,7 +64,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_sheet.html b/docs/reference/write_sheet.html index bbe4f8b..bc06135 100644 --- a/docs/reference/write_sheet.html +++ b/docs/reference/write_sheet.html @@ -70,7 +70,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_summary_charts.html b/docs/reference/write_summary_charts.html index 7da2188..5a3db9f 100644 --- a/docs/reference/write_summary_charts.html +++ b/docs/reference/write_summary_charts.html @@ -66,7 +66,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_summary_report.html b/docs/reference/write_summary_report.html index 82e67bf..151eed5 100644 --- a/docs/reference/write_summary_report.html +++ b/docs/reference/write_summary_report.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/reference/write_summary_sheet.html b/docs/reference/write_summary_sheet.html index 56eba8f..d864969 100644 --- a/docs/reference/write_summary_sheet.html +++ b/docs/reference/write_summary_sheet.html @@ -65,7 +65,7 @@ phenoptrReports - 0.1.0.0 + 0.1.1 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index fabf162..654e42c 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -42,6 +42,9 @@ http://akoyabio.github.io/phenoptrReports/reference/count_phenotypes.html + + http://akoyabio.github.io/phenoptrReports/reference/field_column.html + http://akoyabio.github.io/phenoptrReports/reference/make_nested.html diff --git a/man/field_column.Rd b/man/field_column.Rd new file mode 100644 index 0000000..70c5a18 --- /dev/null +++ b/man/field_column.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utilities.R +\name{field_column} +\alias{field_column} +\title{Get the name of the column that distinguishes fields in a merged cell +seg data file.} +\usage{ +field_column(csd) +} +\arguments{ +\item{csd}{Cell seg data} +} +\value{ +A column name (as a string) +} +\description{ +Get the name of the column that distinguishes fields in a merged cell +seg data file. +}