Error when Running the Tutorial "SeqFish+ Mouse Cortex Example"

[zhli12]

When running Part 14 in the tutorial SeqFish+ Mouse Cortex Example for the new version of Giotto found here https://giottosuite.readthedocs.io/en/latest/subsections/datasets/seqFISH_cortex.html, I cannot load the ligand-receptor file through

LR_data = data.table::fread(system.file("extdata", "mouse_ligand_receptors.txt", package = 'Giotto'))

Error in data.table::fread(system.file("extdata", "mouse_ligand_receptors.txt",  : 
  Input is empty or only contains BOM or terminal control characters

Is the file mouse_ligand_receptors.txt part of the package, or do I need to download it somewhere else?

Below is my system information:

System Information

• MacOS: 12.5
• R 4.2.3
• Giotto 3.3.0
• Python within the Giotto env 3.10.2

[RubD]

Hi @zhli12 we recently moved all the external data to the GiottoData package.

I believe that writing

LR_data = data.table::fread(system.file("extdata", "mouse_ligand_receptors.txt", package = 'GiottoData')) should do the trick. You might have to load the package first library(GiottoData).

Let us know if it worked or not.

[zhli12]

Hi @zhli12 we recently moved all the external data to the GiottoData package.

I believe that writing

LR_data = data.table::fread(system.file("extdata", "mouse_ligand_receptors.txt", package = 'GiottoData')) should do the trick. You might have to load the package first library(GiottoData).

Let us know if it worked or not.

Thank you for your help! I was able to find the data in the GiottoData package.

I just have one more question regarding the tutorial. I'm wondering what is the expected running time for the spatCellCellcom function. I tried to run it this afternoon multiple times on my local system, but the R sessions all crashed in the end. Even running this function using the first 10 ligand-receptor pairs didn't work. Is this function expected to be run on the cluster? Also, is there a way to suppress the series of data.tables produced when running this function exprCellCellCom?

[mattobny]

@zhli12 running on cluster should not be necessary for spatCellCellcom(), although a cluster is preferrable for computing power in most cases. Has R crashed on multiple occasions when running this? We have seen a similar issue, #629, but a version increase of R and Giotto fixed the issue. Since you're already on R 4.2.3, I would think reinstallation may be advisable.

exprCellCellcom() takes a verbose argument, which is TRUE by default - try setting it to FALSE for more output suppression. I am working to reduce console outputs throughout the codebase, which will come in a later update.