createSpaTalk: SpaTalk object

In ZJUFanLab/SpaTalk: Infer Cell-Cell Communication for Spatial Transcriptomics

SpaTalk object

Description

create SpaTalk object using spatial transcriptomics data.

Usage

createSpaTalk(
  st_data,
  st_meta,
  species,
  if_st_is_sc,
  spot_max_cell,
  celltype = NULL
)

Arguments

st_data	A data.frame or matrix or dgCMatrix containing counts of spatial transcriptomics, each column representing a spot or a cell, each row representing a gene.
st_meta	A data.frame containing coordinate of spatial transcriptomics with three columns, namely 'spot', 'x', 'y' for spot-based spatial transcriptomics data or 'cell', 'x', 'y' for single-cell spatial transcriptomics data.
species	A character meaning species of the spatial transcriptomics data.'Human' or 'Mouse'.
if_st_is_sc	A logical meaning if it is single-cell spatial transcriptomics data. TRUE is FALSE.
spot_max_cell	A integer meaning max cell number for each plot to predict. If if_st_sc is FALSE, please determine the spot_max_cell. For 10X (55um), we recommend 30. For Slide-seq, we recommend 1.
celltype	A character containing the cell type of ST data. To skip the deconvolution step and directly infer cell-cell communication, please define the cell type. Default is NULL.

Value

SpaTalk object

ZJUFanLab/SpaTalk documentation built on Jan. 21, 2025, 3:13 p.m.