Package index • cellsight

Building an app

The two functions that make up the standard workflow. makeShinyFiles() writes the app’s data files, then makeShinyCodes() writes the app itself.

makeShinyFiles(): Generate data files required for shiny app
makeShinyCodes(): Generate code files required for shiny app

Configuring metadata

A CellSight config (scConf) is a data.table describing which cell metadata appears in the app, how it is labelled, ordered and coloured. Create one with createConfig(), then refine it with the mod* helpers.

createConfig(): Create a CellSight config data.table
checkConfig(): Checks if CellSight config data.table contains any errors
addMeta(): Add a metadata to be included in the shiny app
delMeta(): Remove a metadata from being included in the shiny app
modMetaName(): Modify the display name of metadata
modLabels(): Modify the legend labels for categorical metadata
modColours(): Modify the colour palette for categorical metadata
modDefault(): Set the default metadata to display
reorderMeta(): Reorder the order in which metadata appear in the shiny app
showOrder(): Shows the order in which metadata will be displayed
showLegend(): Shows the legends for single-cell metadata

Modality-specific writers

makeShinyFiles() dispatches to these based on the object it is given. Call them directly only when you need to write a single modality, or to pass modality-specific arguments.

makeShinyFilesGEX(): Generate data files required for shiny app (scRNA type data)
makeShinyFilesSpatial(): Generate data files required for shiny app (spatial data)
makeShinyFilesATACsignac(): Generate data files required for shiny app (ArchR object)
makeShinyFilesATACarchr(): Generate data files required for shiny app (ArchR object)
makeShinyFilesDEG(): Generate data files required for shiny app (scRNA type data)

HDF5 writers

Lower-level functions that stream expression matrices and data frames into the chunked HDF5 files the generated app reads from.

makeH5fromSeurat(): Make h5 object from Seurat assay data
makeH5fromAnndata(): Make h5 object from Anndata assay
makeH5fromArchR(): Make h5 object from ArchR data
write_df_chunked_hdf5r(): Write Data Frame to HDF5 File in Chunks using hdf5r

Template helpers

Used by the code writers to render the bundled jinjar templates. Of interest mainly to contributors - see vignette("templates", package = "cellsight").

scJinjaCfg(): jinjar configuration used by all cellsight code writers
scTrim(): Dedent a template block