diff --git a/DESCRIPTION b/DESCRIPTION index 050f1ab..8065881 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: phenoptrReports Title: Create reports using Phenoptics data -Version: 0.1.3.9000 +Version: 0.1.4 Date: 2018-11-05 Authors@R: c( person("Kent S", "Johnson", role = c("aut", "cre"), @@ -39,7 +39,7 @@ Remotes: akoyabio/phenoptr, hms-dbmi/UpSetR Roxygen: list(markdown = TRUE) -RoxygenNote: 6.1.0 +RoxygenNote: 6.1.1 Suggests: ggridges, testthat diff --git a/NEWS.md b/NEWS.md index b448522..6be118c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,11 @@ -# phenoptrReports 0.1.3.9000 +# phenoptrReports 0.1.4 +**2018-12-04** +New features: +- Component levels report shows signal levels of bright and dark pixels + in multiplex images. + +Misc: - Unmixing quality report works when DAPI and AF components are not present. - `consolidate_and_summarize_cell_seg_data` processes files pairwise for reduced memory requirements. diff --git a/_pkgdown.yml b/_pkgdown.yml index 432aca3..69d289d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -12,12 +12,12 @@ navbar: href: index.html - text: "Tutorials" menu: - - text: "Unmixing quality report" - href: articles/unmixing_quality_report.html - text: "Consolidating inForm data" href: articles/consolidation.html - text: "Analyzing inForm data" href: articles/analysis.html + - text: "Unmixing quality report" + href: articles/unmixing_quality_report.html - text: "Reference" href: reference/index.html right: diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 9bcd8ce..edd09fb 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -8,20 +8,18 @@ License • phenoptrReports - - - + - + - + - + @@ -37,7 +35,8 @@ - + + - - + + + - @@ -31,7 +30,7 @@ phenoptrReports - 0.1.3 + 0.1.4 @@ -51,14 +50,14 @@
  • @@ -95,7 +94,7 @@

    Analyzing inForm data

    Kent Johnson

    -

    2018-11-05

    +

    2018-12-04

    Source: vignettes/analysis.Rmd @@ -243,9 +242,8 @@

    -

    Site built with pkgdown.

    +

    Site built with pkgdown 1.2.0.

    - diff --git a/docs/articles/consolidation.html b/docs/articles/consolidation.html index bd27aa3..bb8790e 100644 --- a/docs/articles/consolidation.html +++ b/docs/articles/consolidation.html @@ -6,14 +6,13 @@ Consolidating inForm data • phenoptrReports - - - - + + + - @@ -31,7 +30,7 @@ phenoptrReports - 0.1.3 + 0.1.4 @@ -51,14 +50,14 @@

  • @@ -95,7 +94,7 @@

    Consolidating inForm data

    Kent Johnson

    -

    2018-11-05

    +

    2018-12-04

    Source: vignettes/consolidation.Rmd @@ -236,9 +235,8 @@

    -

    Site built with pkgdown.

    +

    Site built with pkgdown 1.2.0.

    - diff --git a/docs/articles/index.html b/docs/articles/index.html index 2352a10..05dae59 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -8,20 +8,18 @@ Articles • phenoptrReports - - - + - + - + - + @@ -37,7 +35,8 @@ - + + - - + + + - @@ -31,7 +30,7 @@ phenoptrReports - 0.1.3 + 0.1.4 @@ -51,14 +50,14 @@

  • @@ -95,7 +94,7 @@

    Unmixing quality report

    Kent Johnson

    -

    2018-11-05

    +

    2018-12-04

    Source: vignettes/unmixing_quality_report.Rmd @@ -174,9 +173,8 @@

    -

    Site built with pkgdown.

    +

    Site built with pkgdown 1.2.0.

    - diff --git a/docs/authors.html b/docs/authors.html index 1ca6386..845a030 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -8,20 +8,18 @@ Authors • phenoptrReports - - - + - + - + - + @@ -37,7 +35,8 @@ - + + - - + + + - @@ -31,7 +30,7 @@ phenoptrReports - 0.1.3 + 0.1.4 @@ -51,14 +50,14 @@

  • @@ -91,7 +90,7 @@
    -
    +

    phenoptrReports

    @@ -120,6 +119,11 @@

    Unmixing quality report

    The unmixing quality report analyzes unmixed, singleplex images to help evaluate staining and unmixing quality. This report shows crosstalk between components and highlights potential problem areas in assay development.

    +
    +
    +

    +Component levels report

    +

    The component levels report analyzes unmixed, multiplex images to help evaluate staining levels for an entire experiment. This report shows the distribution of signal and dark pixels for all components.

    phenoptrReports is part of the Akoya Biosciences Phenoptics™ family of Quantitative Pathology Research Solutions. For more information visit the Phenoptics™ home page.

    @@ -218,9 +222,8 @@

    Developers

    -

    Site built with pkgdown.

    +

    Site built with pkgdown 1.2.0.

    -
    diff --git a/docs/news/index.html b/docs/news/index.html index 7673e7b..6a339b4 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -8,20 +8,18 @@ Changelog • phenoptrReports - - - + - + - + - + @@ -37,7 +35,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + + + + + + + + +Merge cell seg data files — addin_10_merge • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Merge cell seg data files

    + Source: R/merge_gadget_addin.R + +
    + +
    + +

    addin_10_merge opens a GUI that allows you to select a directory containing +cell seg data files from multiple, individual fields. The selected files +will be merged +to a single file which is saved to the source directory. +This is similar to the function of the inForm Merge tab but +does not include the ability to review and reject individual fields.

    + +
    + + 
    addin_10_merge()
    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/addin_20_consolidate.html b/docs/reference/addin_20_consolidate.html new file mode 100644 index 0000000..2a61b7d --- /dev/null +++ b/docs/reference/addin_20_consolidate.html @@ -0,0 +1,172 @@ + + + + + + + + +Consolidate and summarize cell seg data files — addin_20_consolidate • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Consolidate and summarize cell seg data files

    + Source: R/consolidate_gadget_addin.R + +
    + +
    + +

    addin_20_consolidate opens a GUI that allows you to select multiple +cell seg data files. The selected files will be consolidated +to a single file which is saved to an output directory +along with summary reports for each file.

    + +
    + + 
    addin_20_consolidate()
    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/addin_30_analysis_app.html b/docs/reference/addin_30_analysis_app.html new file mode 100644 index 0000000..5360529 --- /dev/null +++ b/docs/reference/addin_30_analysis_app.html @@ -0,0 +1,168 @@ + + + + + + + + +Run the Analysis app — addin_30_analysis_app • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Run the Analysis app

    + Source: R/analysis_app.R + +
    + +
    + +

    Runs a Shiny app which will read a consolidated data file and +create aggregated statistics from it.

    + +
    + + 
    addin_30_analysis_app()
    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/addin_40_unmixing_quality.html b/docs/reference/addin_40_unmixing_quality.html new file mode 100644 index 0000000..e9a498b --- /dev/null +++ b/docs/reference/addin_40_unmixing_quality.html @@ -0,0 +1,181 @@ + + + + + + + + +Generate an unmixing quality (crosstalk) report for a selected export folder. — addin_40_unmixing_quality • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Generate an unmixing quality (crosstalk) report for a selected export folder.

    + Source: R/unmixing_quality_addin.R + +
    + +
    + +

    addin_40_unmixing_quality opens a GUI that allows you to select +an export folder containing component data files for singleplex samples. +An unmixing quality report is created for the samples and saved in +the source directory.

    + +
    + + 
    addin_40_unmixing_quality()
    + +

    Details

    + +

    The report generator tries to identify the Opal fluor for each source file +by looking at the file name. It recognizes "DAPI", "AF", "Opalnnn", +and "Opal_nnn". +It also recognizes three leading digits as the number of an Opal fluor.

    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/addin_50_component_levels.html b/docs/reference/addin_50_component_levels.html new file mode 100644 index 0000000..e028d44 --- /dev/null +++ b/docs/reference/addin_50_component_levels.html @@ -0,0 +1,172 @@ + + + + + + + + +Generate a component levels report for a selected export folder. — addin_50_component_levels • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Generate a component levels report for a selected export folder.

    + Source: R/component_levels_addin.R + +
    + +
    + +

    addin_50_component_levels opens a GUI that allows you to select +an export folder containing component data files for multiplex samples. +A component levels report is created for the samples and saved in +the export directory.

    + +
    + + 
    addin_50_component_levels()
    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/check_phenotypes.html b/docs/reference/check_phenotypes.html index 6d704b3..9a6b46b 100644 --- a/docs/reference/check_phenotypes.html +++ b/docs/reference/check_phenotypes.html @@ -8,20 +8,18 @@ Check that all requested phenotypes are defined — check_phenotypes • phenoptrReports - - - + - + - + - + @@ -40,7 +38,8 @@ - + + + + + + + + + +Create a component levels report for multiplex samples — component_levels_report • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Create a component levels report for multiplex samples

    + Source: R/reports.R + +
    + +
    + +

    export_path should be the path to +an export folder containing component data files for multiplex samples. +A component levels report is created for the samples and saved in +the source directory.

    + +
    + + 
    component_levels_report(export_path = NULL)
    + +

    Arguments

    + + + + + + +
    export_path

    Path to a directory containing component_data files.

    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/compute_density_from_cell_summary.html b/docs/reference/compute_density_from_cell_summary.html index 657955f..f21355e 100644 --- a/docs/reference/compute_density_from_cell_summary.html +++ b/docs/reference/compute_density_from_cell_summary.html @@ -8,20 +8,18 @@ Compute cell densities from counts and tissue area — compute_density_from_cell_summary • phenoptrReports - - - + - + - + - + @@ -41,7 +39,8 @@ - + + - + - + - + - + @@ -41,7 +39,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -42,7 +40,8 @@ - + + - + - + - + - + @@ -41,7 +39,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -36,15 +34,15 @@ - + - + + - + - + - + - + @@ -42,7 +40,8 @@ - + + - + - + - + - + @@ -42,7 +40,8 @@ - + + - + - + - + - + @@ -43,7 +41,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -37,7 +35,8 @@ - + + - + - + - + - + @@ -43,7 +41,8 @@ - + + - + - + - + - + @@ -43,7 +41,8 @@ - + + - + - + - + - + @@ -42,7 +40,8 @@ - + + - + - + - + - + @@ -46,7 +44,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -41,7 +39,8 @@ - + + - + - + - + - + @@ -43,7 +41,8 @@ - + + - + - + - + - + @@ -41,7 +39,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + + + + + + + + +Check that a user-specified phenotype definition +can be formed from available phenotypes. — validate_phenotype_definitions • phenoptrReports + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Check that a user-specified phenotype definition +can be formed from available phenotypes.

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

    Check that a user-specified phenotype definition +can be formed from available phenotypes.

    + +
    + + 
    validate_phenotype_definitions(pheno, available)
    + +

    Arguments

    + + + + + + + + + + +
    pheno

    Text destription of a phenotype, +for phenoptr::parse_phenotypes.

    available

    A character vector of available phenotypes

    + +

    Value

    + +

    An error message or empty string

    + + +
    + +
    + +
    +
    +

    Developed by Kent S Johnson.

    +
    + +
    +

    Site built with pkgdown 1.2.0.

    +
    +
    +
    + + + + + + diff --git a/docs/reference/write_counts_sheet.html b/docs/reference/write_counts_sheet.html index bd9066b..89c32dc 100644 --- a/docs/reference/write_counts_sheet.html +++ b/docs/reference/write_counts_sheet.html @@ -8,20 +8,18 @@ Write a cell counts table to an Excel workbook — write_counts_sheet • phenoptrReports - - - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -40,7 +38,8 @@ - + + - + - + - + - + @@ -46,7 +44,8 @@ - + + - + - + - + - + @@ -42,7 +40,8 @@ - + + - + - + - + - + @@ -41,7 +39,8 @@ - + + - + - + - + - + @@ -41,7 +39,8 @@ - + +