Could you please example the data folder structure?

[joe-jhou2]

I have h5 file, json, lowers and position list files stored in the same folder: '/Users/xxx/Documents/Jia10X/V11'
however, when I load the sample by the code below, says the error File does not exist or is non-readable.
Thanks.

dataDir <- '/Users/xxx/Documents/Jia10X'

A1

A1 = createGiottoVisiumObject(
visium_dir = paste0(dataDir,'/V11'),
expr_data = 'filter',
png_name = 'tissue_lowres_image.png',
gene_column_index = 2,
instructions = instrs
)

[RubD]

It looks like you need to start from the h5 file, see details section of https://rubd.github.io/Giotto_site/reference/createGiottoVisiumObject.html. Your current command starts from a structured visium directory.

[joe-jhou2]

it seems " h5_json_scalefactors_path" also required but not in the variable list. after adding this, it loads data

[JunxiangXu]

Hi mimisikai

The createGiottoVisiumObject will automatically read expression matrix and spatial information through the following folder structure:

. visium_dir
|-- raw_feature_bc_matrix
| |-- barcodes.tsv.gz
| |-- features.tsv.gz
| |-- matrix.mtx.gz
|---
|-- spatial
| |--aligned_fiducials.jpg
| |-- detected_tissue_image.jpg
| |--scalefactors_json.json
| |--tissue_hires_image.png
| |--tissue_lowres_image.png
| |--tissue_positions_list.csv

Or alternatively you can start with the h5 file by providing the following arguments:

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

The first one should be found in the result directory of spaceranger output folder and the rest should be found in the spatial directory under it.

[RubD]

@JunxiangXu thanks for providing additional info. Would it help if we separate the createGiottoVisiumObject into createGiottoVisiumObjectH5 and createGiottoVisiumObjectDir? We could still keep the original function as a wrapper around those two, but that might help with potential confusion.