NEWS.md
2020-11-11
read_cell_seg_data
determines column types to prevent errors in some edge cases.make_ppp
to work correctly when given compound phenotypes such as “CD8+/PD-L1+”2020-08-22
make_ppp
function to create marked point patterns.parse_phenotypes
makes nicer names for expression-based phenotypes.phenotype_columns
in support of akoyabio/phenoptrReports#36.read_field_info
and get_map_path
functions.2020-02-28
read_cell_data
more robust against data with comma as the decimal separator.count_touching_cells_fast
.2019-10-22
count_touching_cells_fast
for phenoptrReports spatial map viewer.select_rows()
; return FALSE
instead.2019-06-11
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.2019-05-31
Bug fixes:
density_bands
to work with cell seg data in microns with slide origin (#10).2019-05-10
New feature (and breaking change):
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).count_touching_cells
ignores phenotype pairs of self to self with a warning because the touching algorithm does not handle this case (#7).2019-04-22
Failed with error: ‘there is no package called ‘rtree’’
message that requireNamespace('rtree')
generates (#5).2019-04-12
New features:
count_within_many
and count_within_batch
using akoyabio/rtree
package.count_within_detail
to give per-cell counts.Bug fixes:
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).spatial_distribution_report
vignette and example to use phenoptrExamples
, which contains the required component data file (#3).count_touching_cells
when there is exactly one touching cell pair (#4)2019-03-03
count_within_many
in support of phenoptrReports.count_within
does not count self when ‘from’ and ‘to’ phenotypes are the same.field_column
(moved from phenoptrReports) and validate_phenotypes
.compute_all_nearest_distance
to recognize “Annotation ID” as a field name.2019-02-08
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
sq microns
and sq mm
to square microns
and square mm
to match inForm output.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.read_cell_seg_data
#9
count_within
won’t complain if the data doesn’t have a Sample Name
column.2018-09-28
2018-09-28
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.2018-07-11
count_touching_cells
to work with two-pixel-wide membrane map. #82018-04-24
count_within_batch
to work with cell seg files which don’t have Slide ID
fields.density_at_distance
and density_bands
to estimate cell density at a distance from a boundary.pixels_per_micron="auto"
option to read_cell_seg_data()
.informr
to phenoptr
.subset_distance_matrix
in a backwards-incompatible way. This was done to put the csd
parameter first, matching other functions with a csd
parameter.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.