plexora project set
Answer a question about a registered project.
Usage
plexora project set [-h] [--name NAME] [--segmentation SEGMENTATION] [--data DATA]
[--table TABLE] [--subset COLUMN=VALUE] [--cell-id CELL_ID] [--x X]
[--y Y] [--z Z] [--sample SAMPLE] [--celltype CELLTYPE]
[--markers COLUMN [COLUMN ...]] [--metadata COLUMN [COLUMN ...]]
[--layer LAYER] [--log1p] [--single-image] [--row-number-ids]
[--channel-names NAME [NAME ...]]
[--image-type {brightfield,fluorescence}] [--copy] [--node NAME]
[--dataset DATASET] [--from SPEC.json] [--json]
nameArguments
namerequiredOptions
--name NAMEWhat to call the project. Defaults to the image's filename.
--segmentation SEGMENTATIONA segmentation mask to attach.
--data DATAA feature table: CSV, Parquet, AnnData (.h5ad) or SpatialData (.zarr).
--table TABLEWhich table inside a .zarr store holds the cells. Optional -- Plexora asks when something needs it.
--subset COLUMN=VALUEWhich image, for a table that spans several.
--cell-id CELL_IDThe column holding the cell identifier.
--x XThe column holding the X coordinate.
--y YThe column holding the Y coordinate.
--z ZThe column holding the Z coordinate (each cell's plane), for a table over a z-stack.
--sample SAMPLEThe column holding the image or sample id.
--celltype CELLTYPEThe column holding a phenotype or cell type.
--markers COLUMN [COLUMN ...]Columns holding marker intensities. Naming one of the two lists is enough -- the columns left over become the other.
--metadata COLUMN [COLUMN ...]Columns describing the cells rather than measuring them. Naming one of the two lists is enough -- the columns left over become the other.
--layer LAYERWhich matrix to read intensities from, for AnnData.
--log1pLog-transform the intensities as they are read.
--single-imageThis table covers exactly one image.
--row-number-idsNumber the rows instead of reading an id column.
--channel-names NAME [NAME ...]One per image channel, in order.
--image-type {brightfield,fluorescence}one of: brightfield, fluorescenceOverride how the image is read.
--copyCopy the files into the project directory.
--node NAMEThe data node the files are on, for any path that does not say for itself. In a spec file, {"path": ..., "node": null} keeps one file on this machine.
--dataset DATASETMove it into this dataset.
--from SPEC.json--jsonExamples
Say which columns are markers
plexora project set slide --markers CD3 CD8 CD20Add a cell table later
plexora project set slide --data cells.csvMove the project into a dataset
plexora project set slide --dataset "Melanoma cohort"Python equivalent
import plexora
plexora.configure_project("slide", markers=["CD3", "CD8", "CD20"])