Create a giotto object from 10x visium data#

Last Updated: Sep 07, 2023

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#

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

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