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.NA
values in distance columns of cell seg tables.
Previously NA
values could cause the column to be read as character data.read_maps
will find the correct path when given a cell seg table path.lintr
and goodpractices
.compute_all_nearest_distance
is a convenience function which reads a
cell seg table, adds Distance to <phenotype>
columns, and writes it out
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