Changelog

phenoptr 0.1.5

2019-03-03

  • Add count_within_many in support of phenoptrReports.
  • count_within does not count self when ‘from’ and ‘to’ phenotypes are the same.
  • Add field_column (moved from phenoptrReports) and validate_phenotypes.
  • Fix compute_all_nearest_distance to recognize “Annotation ID” as a field name.

phenoptr 0.1.4

2019-02-08

  • Update find_nearest_distance, compute_all_nearest_distance, density_at_distance, density_bands, count_within and spatial_distribution_report to work with consolidated data from phenoptrReports (#1).

Bug fixes

  • Change sq microns and sq mm to square microns and square mm to match inForm output.

phenoptr 0.1.3

2018-12-27

  • spatial_distribution_report works correctly with cell seg data in microns. To do so, it requires a component data file for the target field. Image dimensions are taken from that file.
  • count_touching_cells works correctly when cell seg data is in microns.
  • Require readr version 1.2.0 or higher to avoid incorrectly reading numeric data columns as integer.
  • Add a simple data quality check to read_cell_seg_data #9
  • count_within won’t complain if the data doesn’t have a Sample Name column.
  • More accurate image location from component file if PerkinElmer tiff library is available.

phenoptr 0.1.2

2018-10-29

  • Update link to Phenoptics home page.

phenoptr 0.1.1.9007

2018-09-28

  • Remove import dependency on tidyverse. Examples and vignettes use dplyr, ggplot2 and magrittr instead. #6

phenoptr 0.1.1.9006

2018-09-28

  • New parse_phenotypes function simplifies creation of selectors for select_rows.
  • select_rows recognizes the column format of phenotype-per-marker data.
  • select_rows treats a NA selector as “select all”. This is helpful in lists of selectors.
  • read_cell_seg_data attempts to skip microns conversion if it was already done.

phenoptr 0.1.1.9005

2018-07-11

  • Fix count_touching_cells to work with two-pixel-wide membrane map. #8

phenoptr 0.1.1.9004

2018-04-24

  • Fix count_within_batch to work with cell seg files which don’t have Slide ID fields.

phenoptr 0.1.1.9003

  • Add density_at_distance and density_bands to estimate cell density at a distance from a boundary.

phenoptr 0.1.1.9002

phenoptr 0.1.1.9001

  • Faster count_touching_cells when EBImage 4.19.9 is available.

phenoptr 0.1.1.9000

Backwards incompatible changes

  • Renamed the package from informr to phenoptr.
  • This version changed the order of arguments to subset_distance_matrix in a backwards-incompatible way. This was done to put the csd parameter first, matching other functions with a csd parameter.

New features

  • spatial_distribution_report creates an HTML report showing the location and nearest-neighbor relations of cells in a single field.
  • count_touching_cells uses morphological analysis of nuclear and membrane segmentation maps to find touching cells of paired phenotypes.
  • read_components reads component image files.
  • count_within and count_within_batch count the number of from cells having a to cell within a given radius.
  • list_cell_seg_files lists all cell seg data files in a folder.
  • Added vignettes
    • “Reading and Exploring inForm Tables”
    • “Reading and Displaying inForm Image Files”
    • “Computing Inter-cellular Distances”
    • “Find and count touching cells”
    • “Selecting cells within a cell segmentation table”

Bug fixes

  • Better handling of NA values in distance columns of cell seg tables. Previously NA values could cause the column to be read as character data.

Other changes

  • read_maps will find the correct path when given a cell seg table path.
  • Many documentation improvements.
  • Internal cleanup using lintr and goodpractices.
  • zlib license

phenoptr 0.1.0.9001

New features

  • compute_all_nearest_distance is a convenience function which reads a cell seg table, adds Distance to <phenotype> columns, and writes it out again.