About loading 10X data

[Pedramto89]

I wanted to load a filtered data from a spatial 10X experiment by:

se <- SpatialExperiment::read10xVisium(samples = "outs/filtered_feature_bc_matrix.h5", type = "sparse", data = "filtered")

However, I get en error: Error in SpatialExperiment::read10xVisium(samples = "outs/filtered_feature_bc_matrix.h5", : No matching files found for 'images=c(“lowres”)

I tried to change the code to: se <- SpatialExperiment::read10xVisium(samples = "outs/filtered_feature_bc_matrix.h5", type = "sparse", data = "filtered", images = c("lowres"), load = TRUE) but didn't work. What would I do?

Thanks

[AteeqMKhaliq]

Hi, I think its not finding the images (H&E) folder. please verify if you have a "spatial" folder in "outs" folder. for example /spatial_analysis/spaceranger_samples/sample1/outs/spatial/ in the spatial folder you should have lowres.png as /spatial_analysis/spaceranger_samples/sample1/outs/spatial/tissue_lowres_image.png if you don't have tissue_lowres_image.png then you will get this error. regards, AMK PS: I am the User of this wonderful package.

[Pedramto89]

@AteeqMKhaliq Thank you for your response. So, there is a "spatial" folder in the "outs" from spaceranger and the image is there. I tried to set the directory for it but it again gave me the same error:

Error in match.arg(images, imgs, several.ok = TRUE) : 'arg' should be one of “lowres”, “hires”, “detected”, “aligned”

[bmill3r]

Hi @Pedramto89 (and thanks for your help @AteeqMKhaliq!)

In the tutorial Analysis of 10X Visium data, there is an example of using the function SpatialExperiment::read10xVisium(). I think the issue is that you are setting the parameter samples equal to a file, when instead it needs to be a directory. See the manual page for more details. For example, I believe you want to instead set samples = "outs/", which should be a directory that contains not only the filtered_feature_bc_matrix.h5 but also the subdirectory "spatial" that contains the images that this function is looking for.

Let me know if this helps or if you are still having problems, Brendan

[Pedramto89]

Hi @bmill3r Thank you for your response. I understand it should be in the correct directory. That is why I set the directory already to the existing files and folders. The current working directory is this: "/Users/pedram/Documents/MASTER/Thesis/Visium/Data_Analysis/Res_of_Seq/9137/9137A/outs"

But again, I get the error again with this code: se <- SpatialExperiment::read10xVisium(samples = "filtered_feature_bc_matrix.h5", type = "sparse", data = "filtered", images = "spatial/tissue_lowres_image.png", load = TRUE)

The Error:

Error in match.arg(images, imgs, several.ok = TRUE) : 'arg' should be one of “lowres”, “hires”, “detected”, “aligned”

[bmill3r]

Hi @Pedramto89,

Based on the manual for SpatialExperiment::read10xVisium() I think that the parameter "samples" actually needs to be set to the directory itself and not to a specific file. And to be safe I also recommend using absolute paths when pointing functions to directories or files. What happens if you try:

se <- SpatialExperiment::read10xVisium(
        samples = "/Users/pedram/Documents/MASTER/Thesis/Visium/Data_Analysis/Res_of_Seq/9137/9137A/outs/",
        type = "sparse",
        data = "filtered",
        images = "lowres",
        load = TRUE
)

Let me know if that helps, Brendan

[Pedramto89]

Thank you @bmill3r It finally worked. It seems the absolute path was the problem. For any reason, it didn't work before.