Error using reader functio to import VisiumHD data

[jade-minzlaff]

Describe the Error

Hi, I am attempting to follow the workflow demonstrated for VisiumHD analysis in Giotto here: https://drieslab.github.io/Giotto_website/articles/VisiumHD_Human_Colorectal_Cancer.html
To analyze my VisiumHD data with Giotto.

However, despite using the correct Visium HD output folder specified, I get an error when I try to import the Visium HD data. My code:

provide path to visium folder

data_path <- "C:/Users/jadem/OneDrive/Desktop/Batch1_Reanalysis_112524/analysis/spaceranger/FN691/H1-34J9CJZ_A1_FN691_mGEXv2HD/outs/binned_outputs/square_008um"

readerHD <- importVisiumHD()

readerHD$data_path <- data_path

...

Error Message

readerHD$data_path <- data_path
Error in $<-(*tmp*, data_path, value = "C:/Users/jadem/OneDrive/Desktop/Batch1_Reanalysis_112524/analysis/spaceranger/FN691/H1-34J9CJZ_A1_FN691_mGEXv2HD/outs/binned_outputs/square_008um") :
Only items in 'visiumHD_dir', 'expression_source', 'gene_column_index', 'barcodes', 'array_subset_row', 'array_subset_col', 'pxl_subset_row', 'pxl_subset_col' can be set

# Your error message here

To Reproduce

Steps to reproduce the behavior, i.e.:

1. Following tutorial file '...'
2. Download data '...'
3. Run function(s) '...'
4. See error

Expected behavior

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Screenshots

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System Information
Please replace the following according to your machine:

platform x86_64-w64-mingw32
arch x86_64
os mingw32
crt ucrt
system x86_64, mingw32
status
major 4
minor 4.2
year 2024
month 10
day 31
svn rev 87279
language R
version.string R version 4.4.2 (2024-10-31 ucrt)
nickname Pile of Leaves
[1] ‘4.1.6’
Additional context

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[iqraAmin]

Hi @jade-minzlaff,

Apologies for the inconvenience. I will update the vignette as the data_path argument has been replaced by visiumHD_dir. Please use readerHD$visiumHD_dir instead. To create a Giotto object, you can use the following code:

visiumHD <- readerHD$create_gobject(
    visiumHD_dir = data_path,
    png_name = "tissue_lowres_image.png",
    gene_column_index = 2)

[jade-minzlaff]

Hi Iqra Amin,

Thank you for your reply, but unfortunately when I use the code chunk you sent, I receive the error: "Error: attempt to apply non-function"

When I add in the other arguments in the Giotto tutorial to what you sent above, I get a similar error message:

For the code:

createGiottoVisiumHDObject(
visiumHD <- readerHD$create_gobject(
visiumHD_dir = data_path,
png_name = "tissue_lowres_image.png",
gene_column_index = 2,
instructions = NULL,
expression_matrix_class = c("dgCMatrix", "DelayedArray"),
cores = NA,
verbose = FALSE)
)

I get the error: "Error in createGiottoVisiumHDObject(visiumHD <- readerHD$create_gobject(visiumHD_dir = data_path, :
attempt to apply non-function"

[iqraAmin]

Hi @jade-minzlaff, createGiottoVisiumHDObject() takes visiumHD directory path as input. You can check the arguments for the function using ?createGiottoVisiumHDObject(). You can use createGiottoVisiumHDObject() as following:

Giotto::createGiottoVisiumHDObject(visiumHD_dir = "path_to_data", 
                                   expr_data = c("raw", "filter"),
                                   gene_column_index = 1)

To use visium HD reader function, use the following.

visiumHD_dir <- "/path/to/data/"
readerHD <- importVisiumHD()
readerHD$visiumHD_dir <- visiumHD_dir
visiumHD <- readerHD$create_gobject(
  visiumHD_dir = visiumHD_dir,
  png_name = 'tissue_lowres_image.png',
  gene_column_index = 2
)

You can use any of the above approaches. Let me know if they work or if you still encounter any issues.

[jade-minzlaff]

Hi @iqraAmin,

Thank you again for responding. Unfortunately, both of those options still result in errors for me.

Using the createGiottoVisiumHDObject:

provide path to visium folder

data_path <- "C:/Users/jadem/OneDrive/Desktop/Batch1_Reanalysis_112524/analysis/spaceranger/FN691/H1-34J9CJZ_A1_FN691_mGEXv2HD/outs/binned_outputs/square_008um"
Giotto::createGiottoVisiumHDObject(visiumHD_dir = "data_path",
expr_data = c("raw", "filter"),
gene_column_index = 1)

Error:
Warning: filtered_feature_bc_matrix not detected in visiumHD directoryWarning: raw_feature_bc_matrix not detected in visiumHD directoryWarning: spatial not detected in visiumHD directoryA structured visium directory will be used
Error: [Giotto]
path needs to be a path to a visium directory

The path I am giving it to the Visium outout folder which contains filtered_feature_bc_matrix.h5 and raw_feature_bc_matrix.h5 files, despite this error message.

Using the visium HD reader function:

visiumHD_dir <- "C:/Users/jadem/OneDrive/Desktop/Batch1_Reanalysis_112524/analysis/spaceranger/FN691/H1-34J9CJZ_A1_FN691_mGEXv2HD/outs/binned_outputs/square_008um"
readerHD <- importVisiumHD()
readerHD$visiumHD_dir <- visiumHD_dir
visiumHD <- readerHD$create_gobject(
visiumHD_dir = visiumHD_dir,
png_name = 'tissue_lowres_image.png',
gene_column_index = 2
)

Error:
Error in data.table::fread(input = paste0(path_to_data, "/", features_file), :
input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http[s]://', 'ftp[s]://' or 'file://', or, the input data itself containing at least one \n or \r

Do you have any further suggestions? Thank you again for your responsiveness.