Convert Seurat object to STID object — CreateSTIDObject • STID

Creates an STID object from a Seurat object with infection-specific metadata.

Usage

CreateSTIDObject(
  seurat_obj = NULL,
  host_org = NULL,
  pathogen_grp = NULL,
  pathogen_org = NULL,
  samp_colnm = NULL,
  samp_grp_colnm = NULL,
  celltype_colnm = NULL,
  x_colnm = NULL,
  y_colnm = NULL,
  pathogen_genes = NULL,
  data_format = NULL,
  data_platform = NULL,
  binsize = NULL,
  coord_interval = NULL,
  base_unit = NULL,
  project_id = NULL,
  description = NULL,
  ...
)

Arguments

seurat_obj: A Seurat object to be converted
host_org: Character, host organism - "human", "mouse", or "unknown"
pathogen_grp: Character, pathogen group - "virus", "bacteria", "parasite", or "unknown"
pathogen_org: Character, specific pathogen organism name
samp_colnm: Character, column name in metadata containing sample IDs
samp_grp_colnm: Character, column name in metadata containing sample groups
celltype_colnm: Character, column name in metadata containing cell types
x_colnm: Character, column name for x coordinates
y_colnm: Character, column name for y coordinates
pathogen_genes: Character vector, names of pathogen genes
data_format: Character, data format - "square_grid" or "hex_grid"
data_platform: Character, data platform - "StereoSeq", "Visium", "VisiumHD", "SlideSeq", or "unknown"
binsize: Numeric, bin size for spatial data
coord_interval: Numeric, coordinate coord_interval
base_unit: Numeric, base unit for spatial coordinates, and the unit is mm
project_id: Character, project identifier
description: Character, project description
...: Additional arguments passed to as.STID

Value

An STID object

Examples

if (FALSE) { # \dontrun{
ist_obj <- CreateSTIDObject(
  seurat_obj = seurat_object,
  samp_colnm = "sample_id",
  celltype_colnm = "cell_type",
  host_org = "human",
  pathogen_grp = "virus",
  pathogen_org = "SARS-CoV-2",
  data_format = "square_grid",
  data_platform = "StereoSeq"
)
} # }