processing: Preprocess spatial data

In YeehanXiao/STREAM: STREAM: Spatial Transcriptomics data Analyses and Modeling

Preprocess spatial data

Description

Preprocess spatial data

Usage

processing(object, ...)

## S4 method for signature 'giotto'
processing(
  object,
  expression.values = "raw",
  norm.method = c("standard", "osmFISH"),
  min.cells = 10,
  min.features = 200,
  dims = 1:10,
  resolution = 0.6,
  save.plot = FALSE,
  batch.columns = NULL,
  verbose = FALSE,
  outputFolder = NULL,
  ...
)

Arguments

object	a giotto object
...	Argument passed to other methods
expression.values	expression values to use
norm.method	normalization method to use.
min.cells	minimum of cells to expressed in a gene
min.features	minimum of genes to detected in a cell
dims	number of dimensions to use as input for UMAP
resolution	resolution for leiden cluster
save.plot	directly save the plot [boolean]
batch.columns	metadata columns that represent different batch (max = 2) adjustGiottoMatrix
verbose	verbose
outputFolder	Output folder to save results.

Value

a giotto object

YeehanXiao/STREAM documentation built on Aug. 13, 2022, 6:43 p.m.