createGiottoVisiumObject#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/giotto.R#L2010

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 `createGiottoInstructi ons <#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