createGiottoVisiumObject: createGiottoVisiumObject

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

createGiottoVisiumObject

Description

creates Giotto object directly from a 10X visium folder

Usage

createGiottoVisiumObject(
  visium_dir = NULL,
  expr_data = c("raw", "filter"),
  gene_column_index = 1,
  h5_visium_path = NULL,
  h5_gene_ids = c("symbols", "ensembl"),
  h5_tissue_positions_path = NULL,
  h5_image_png_path = NULL,
  png_name = NULL,
  do_manual_adj = TRUE,
  xmax_adj = 0,
  xmin_adj = 0,
  ymax_adj = 0,
  ymin_adj = 0,
  scale_factor = NULL,
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

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)
h5_visium_path	path to visium 10X .h5 file
h5_gene_ids	gene names as symbols (default) or ensemble gene ids
h5_tissue_positions_path	path to tissue locations (.csv file)
h5_image_png_path	path to tissue .png file (optional)
png_name	select name of png to use (see details)
do_manual_adj	flag to use manual adj values instead of automatic alignment based on visium values
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
scale_factor	scaling of image dimensions relative to spatial coordinates (defaults to visium specified)
instructions	list of instructions or output result from createGiottoInstructions
cores	how many cores or threads to use to read data if paths are provided
verbose	be verbose

Details

If starting from a Visium 10X directory:

• 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)

If starting from a Visium 10X .h5 file

• h5_visium_path: full path to .h5 file: /your/path/to/visium_file.h5

• h5_tissue_positions_path: full path to spatial locations file: /you/path/to/tissue_positions_list.csv

• h5_image_png_path: full path to png: /your/path/to/images/tissue_lowres_image.png

Value

giotto object

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.