NEWS.md

In akoyabio/phenoptr: inForm Helper Functions

phenoptr 0.3.2

2022-01-03

• Fix parse_composite_info to work with older composite images that are missing ImageDescription (akoyabio/phenoptrReports#52)
• Correctly parse phenotype expressions containing slashes (#18)
• Tighten up the column exclusion criteria for read_cell_seg_data with col_select="phenoptrReports" (#16)
• Update tests to work with testthat 3.1.

phenoptr 0.3.1

2021-08-24

• Add read_composites and read_composite_info to read and parse metadata in inForm composite images.

phenoptr 0.3.0

2021-08-03

Misc: - Update dependencies to modern versions - Fix for bug in readr 2.0.0

phenoptr 0.2.10

2021-06-01

Changes to read_cell_seg_data: - Add a col_select parameter to support reading only selected fields, with a 'phenoptrReports' option to read only fields needed by phenoptrReports. - Use vroom::vroom() instead of readr::read_tsv for speed and support of col_select. - For an export file containing all inForm fields, read_cell_seg_data(csd_path, col_select='phenoptrReports') can be 4-5x faster and use 75% less memory for the results, compared to the previous version.

Spatial distribution report: - Fix report generation to work when paths contain spaces.

Misc: - Fix select_rows to always return FALSE instead of NA. - Update to work with CRAN release of tiff 0.1-8 - Update to work with (and require) spatstat 2.0.0 - Require R 4.0.0 or greater for compatibility with latest rtree

phenoptr 0.2.9

2020-11-11

• Improved the way read_cell_seg_data determines column types to prevent errors in some edge cases.
• Fixed make_ppp to work correctly when given compound phenotypes such as "CD8+/PD-L1+"

phenoptr 0.2.8

2020-08-22

• Add make_ppp function to create marked point patterns.
• parse_phenotypes makes nicer names for expression-based phenotypes.
• Add phenotype_columns in support of akoyabio/phenoptrReports#36.
• Add read_field_info and get_map_path functions.

phenoptr 0.2.7

2020-06-02

Fix to work with dplyr 1.0.0.

phenoptr 0.2.6

2020-04-21

• Avoid deprecation warning for expand_scale with ggplot2 version 3.3.0

phenoptr 0.2.5

2020-02-28

• Make read_cell_data more robust against data with comma as the decimal separator.
• Better documentation and error messages in count_touching_cells_fast.

phenoptr 0.2.4

2019-10-22

• Add count_touching_cells_fast for phenoptrReports spatial map viewer.
• Don't return NA values from select_rows(); return FALSE instead.
• Now requires tidyr >= 1.0.0.

phenoptr 0.2.3

2019-08-07

• Add annotation_raster_native for faster plotting with background images.

phenoptr 0.2.2

2019-06-11

• Remove the explicit dependency on phenoptrReports to avoid installation pain. phenoptrReports is still needed to build the vignettes and to run a few of the examples.
• parse_phenotypes and validate_phenotype_definitions support expressions in phenotype definitions.

phenoptr 0.2.1

2019-05-31

• The spatial analysis report now uses the full-intensity composite image as its background image. Connecting lines and the scale bar are white to be visible against the dark background of the composite image.

Bug fixes: - Fix density_bands to work with cell seg data in microns with slide origin (#10).

phenoptr 0.2.0

2019-05-10

New feature (and breaking change): - The nearest neighbor functions compute_all_nearest_distance and find_nearest_distance now create columns containing the Cell ID of the nearest cell, as well as the columns with the actual distance. This column can be used to find the locations of nearest cells and to find mutual nearest neighbors. The "Computing inter-cell distances" tutorial shows some uses of this data.

Bug fixes: - read_cell_seg_data recognizes and correctly reads inForm data which uses comma as the decimal separator (#8). - Fix SpatialDistributionReport to work with more than 8 phenotypes (#6). - count_touching_cells ignores phenotype pairs of self to self with a warning because the touching algorithm does not handle this case (#7).

phenoptr 0.1.6.1

2019-04-22

• Remove the scary Failed with error: ‘there is no package called ‘rtree’’ message that requireNamespace('rtree') generates (#5).

phenoptr 0.1.6

2019-04-12

New features: - Add fast implementation of count_within_many and count_within_batch using akoyabio/rtree package. - Add fast count_within_detail to give per-cell counts.

Bug fixes: - Fix get_field_info to work with the standard (CRAN) tiff package. - count_within and related functions return NA for within_mean when there are no from cells (rather than a mean of 0). - Update spatial_distribution_report vignette and example to use phenoptrExamples, which contains the required component data file (#3). - Fix problem in count_touching_cells when there is exactly one touching cell pair (#4)

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

• Add pixels_per_micron="auto" option to read_cell_seg_data().
• Supports tiled component files using the PerkinElmer fork of the tiff package.

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.

akoyabio/phenoptr documentation built on Jan. 7, 2022, 5:37 p.m.