createGiottoVisiumObject

Create a giotto object from 10x visium data

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,
  h5_json_scalefactors_path = NULL,
  png_name = NULL,
  do_manual_adj = FALSE,
  xmax_adj = 0,
  xmin_adj = 0,
  ymax_adj = 0,
  ymin_adj = 0,
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

Arguments

Argument	Description
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)
h5_json_scalefactors_path	path to .json scalefactors (optional)
png_name	select name of png to use (see details)
do_manual_adj	flag to use manual adj values instead of automatic image alignment
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` <#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)

• the file scalefactors_json.json will be detected automaticated and used to attempt to align the data

  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

• h5_json_scalefactors_path: full path to .json file: /your/path/to/scalefactors_json.json

Value

giotto object