createGiottoVisiumObject: createGiottoVisiumObject

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

creates Giotto object directly from a 10X visium folder

Usage

createGiottoVisiumObject(
  visium_dir = NULL,
  expr_data = c("raw", "filter"),
  gene_column_index = 1,
  png_name = NULL,
  xmax_adj = 0,
  xmin_adj = 0,
  ymax_adj = 0,
  ymin_adj = 0,
  instructions = NULL,
  cores = NA
)

Arguments

visium_dir	path to the 10X visium directory [required]
expr_data	raw or filtered data (see details)
gene_column_index	which column index to select (see details)
png_name	select name of png to use (see details)
xmax_adj	adjustment of the maximum x-value to align the image
xmin_adj	adjustment of the minimum x-value to align the image
ymax_adj	adjustment of the maximum y-value to align the image
ymin_adj	adjustment of the minimum y-value to align the image
instructions	list of instructions or output result from createGiottoInstructions
cores	how many cores or threads to use to read data if paths are provided

Details

• expr_data: raw will take expression data from raw_feature_bc_matrix and filter from filtered_feature_bc_matrix

• gene_column_index: which gene identifiers (names) to use if there are multiple columns (e.g. ensemble and gene symbol)

• png_name: by default the first png will be selected, provide the png name to override this (e.g. myimage.png)

Value

giotto object

Examples

    createGiottoVisiumObject(visium_dir)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.