Package index

Specification

cs_spec_version()

Version of the cellspec specification

cs_vocabulary()

Columns and controlled vocabularies of the cellspec format

Object

cs_new()

Create a cellspec object

cs_cells() cs_measurements() cs_dictionary() cs_images() cs_channels() cs_provenance() cs_adjacency()

Access the components of a cellspec object

cs_features() cs_markers()

Select features and markers by their dictionary entries

is_cellspec()

Test for a cellspec object

Validation

cs_validate() cs_assert_valid()

Validate a cellspec object

cs_feature_support()

Summarise the signal support of features per image

Readers and storage

cs_formats()

List the available cellspec readers

cs_detect_format()

Detect the generic table format

cs_column_map()

Validate a table column map

cs_read()

Read a delimited table into a cellspec object

cs_read_cellspec()

Read a canonical cellspec directory

cs_verify()

Verify a canonical cellspec directory

cs_write()

Write a cellspec directory

cs_bind()

Combine cellspec objects from different images

cs_merge_tiles()

Merge tiled cellspec objects using centroid ownership

cs_read_npy() cs_read_npz() cs_write_npy() cs_write_npz() experimental

Read and write NumPy array files

Signals

cs_signal_policy()

Create a signal selection policy

cs_signal_matrix()

Select one signal per cell and marker

cs_marker_map()

Create a marker-name mapping

cs_read_signal_policy()

Read a signal policy from JSON or CSV

cs_write_signal_policy()

Write a signal policy as JSON or CSV

Interoperability and app

cs_as_spe()

Convert a cellspec object to SpatialExperiment

cs_from_spe()

Convert a SpatialExperiment back to cellspec

cs_as_anndata()

Convert a cellspec object to AnnData

cs_app() stable

Create the cellspec review application

Methods

print(<cellspec>) summary(<cellspec>) print(<cellspec_summary>) dim(<cellspec>)

Print, summarise and measure a cellspec object

as.data.frame(<cellspec>) as_tibble(<cellspec>)

Convert a cellspec object to a data frame

`[`(<cellspec>)

Subset a cellspec object by cells and features

plot(<cellspec>)

Plot cellspec quality-control views

Examples

cs_example()

A small synthetic cellspec object

Package

cellspecR cellspecR-package stable

cellspecR: Read, Validate and Store Multiplexed Imaging Cell Tables