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SpatialMap Settings

createSpatialMapSettings.Rd

The SM Settings object is used to store information, settings, and parameters pertinent to the use of the SpatialMap object

Usage

createSpatialMapSettings(settings.list = NULL)

showsettings(object)

Arguments

settings.list

A list of settings to initialize for a SpatialMap object.

object

A SpatialMap object

Details

  • cores: Number of threads

  • parallel: Which parallel framework to use? "base", "future", or "no"

  • future.initialized: Defaults to FALSE. Whether or not the future framework has been properly initialized.

  • show.progress: Whether to use pbapply to display a progress bar (requires pbapply package)

  • Rstudio: Whether or not you are using Rstudio

  • python.path: Path to use for Python features

  • python.environment: Name of the Conda environment used for Python features

  • python.method: How to handle calls to Python from R? As of 0.4.20 this is deprecated, and all Python in the future will be handled by reticulate

  • local.images: Whether to retrieve and download images locally. Defaults to FALSE

  • data_path: Path to the source data - or, if DB is used, the query string

  • file_paths: List of files in data_path if relevant

  • filtration: Which filtration approach should be used? hard - Cells not passing filter are removed completely soft - Cells not passing filter are removed from analyses, but not spatial analyses rename - Cells not passing filter are reclassified in all downstream analyses

  • normalization: Which normalization approach to use? log - log10(x + 1) arcsinh - arcsinh() with scale factors determined from each marker's distribution cuberoot - x^(1/3) restore - model - fit distributions

  • max_cell.size: Filtration parameter

  • min_cell.size: Filtration parameter

  • max_signal.sum: Filtration parameter

  • min_signal.sum: Filtration parameter

  • max_normalized.signal.sum: Filtration parameter

  • min_normalized.signal.sum: Filtration parameter

  • max_DNA: Filtration parameter. Refers to DAPI or RedDot2 channels

  • min_DNA: Filtration parameter. Refers to DAPI or RedDot2 channels

  • max_num.markers: Filtration parameter

  • min_num.markers: Filtration parameter

  • max_dist.n: Filtration parameter

  • max_dist.smooth: Filtration parameter

  • exclude_partitions: Filtration parameter

  • SpatialMap.version: SpatialMap package version used to create this object.

  • packages: Packages loaded

Functions

  • showsettings():

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