Create a giotto object from 10x visium data

Source: R/convenience_general.R

Create Giotto object directly from a 10X visium folder. Also accepts visium H5 outputs.

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,
  expression_matrix_class = c("dgCMatrix", "DelayedArray"),
  h5_file = NULL,
  cores = NA,
  verbose = NULL
)

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). Image autoscaling looks for matches in the filename for either "hires" or "lowres"

h5_json_scalefactors_path

path to .json scalefactors (optional)

png_name

select name of png to use (see details)

do_manual_adj

deprecated

xmax_adj

deprecated

xmin_adj

deprecated

ymax_adj

deprecated

ymin_adj

deprecated

instructions

list of instructions or output result from createGiottoInstructions

expression_matrix_class

class of expression matrix to use (e.g. "dgCMatrix", "DelayedArray")

h5_file

optional path to create an on-disk h5 file

cores

how many cores or threads to use to read data if paths are provided

verbose

be verbose

Value

giotto object

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 automatically 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