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Generates PCA analysis results for a SpaMTP Seurat Object

Source: R/SpatialAnalysis.R
RunMetabolicPCA.Rd

This function run PCA analaysis on a SpaMTP Seurat Object. The user can provide a bin/resolution size to increase the bin size and reduce the dimensionality/noise of the SM dataset prior to calculating PCAs.

Usage

RunMetabolicPCA(
  SpaMTP,
  npcs = 30,
  variance_explained_threshold = 0.9,
  assay = "SPM",
  slot = "counts",
  show_variance_plot = FALSE,
  bin_resolution = NULL,
  resolution_units = "ppm",
  bin_method = "sum",
  reduction.name = "pca",
  verbose = TRUE
)

Arguments

SpaMTP

SpaMTP Seurat class object that contains spatial metabolic information.

npcs

is an integer value to indicated preferred number of PCs to retain (default = 30).

variance_explained_threshold

Numeric value defining the explained variance threshold (default = 0.9).

assay

Character string defining the SpaMTP assay to extract intensity values from (default = "SPM").

slot

Character string defining the assay slot containing the intensity values (default = "counts").

show_variance_plot

Boolean indicating weather to display the variance plot output by this analysis (default = FALSE).

bin_resolution

Numeric value defining the resolution to use for binning m/z peaks. If set to NULL, no binning will be performed (default = NULL).

resolution_units

Character string specifying the units of the bin_resolution. Either 'ppm' or 'mz' can be provided. bin_resolution must be provided for this parameter to be implemented (default = "ppm").

bin_method

Character string defining the method to use for binning respective m/z peaks that fall within a bin. Options for this parameter can be one of "sum", "mean", "max" or "min". bin_resolution must be provided for this parameter to be implemented (default = "sum").

reduction.name

Character string indicating the name associated with the PCA results stored in the output SpaMTP Seurat object (default = "pca").

verbose

Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Value

SpaMTP object with pca results stored in the

Examples

# HELPER FUNCTION