Potential issues in data_process function in R_utils.R

[bsungwoo]

Hello,

Thank you for providing a nice tool for decomposing cellular composition in spatial transcriptomic data. I was trying to utilize DSTG for my Visium spatial transcriptomics dataset and ran into an error.

The error occurred when I was running the below command in the Ubuntu terminal with R version 4.0.3.

Rscript convert_data.R scRNAseq_data.RDS spatial_data.RDS scRNAseq_label.RDS

I created a count matrix of single-cell data for scRNAseq_data.RDS (dim: total number of genes * total number of cells), a count matrix for spatial data for spatial_data.RDS (dim: total number of genes * total number of spatial spots) and a cell type label for each cell barcode (dim: total number of cells * 1) for scRNAseq_label.RDS.

The error message told me that in line 110 in R_utils.R, "st_labels" is not defined.

label.list2 <- do.call("rbind", rep(list(st_labels[[1]]), round(N2/N1)+1))[1:N2]

I presumed that since "st_labels" is defined in the next line (111), fixing st_labels[[1]] to st_label[[1]] may resolve the issue. Or is there any problem with my input for the convert_data.R?

Could you kindly check-up with the data_process function in R_utils.R?

Thanks a lot for creating the nice tool!

[bsungwoo]

When I changed "st_labels" to "st_label" in line 110 of R_utils.R, another error message appeared in the same line.

run real data...
[1] "Generating synthetic test spots..."
|======================================================================| 100%
[1] "Generation of 1000 test spots took 0.21 mins"
[1] "output consists of a list with two dataframes, this first one has the weighted count matrix and the second has the metadata for each spot"
Error in [.data.frame(do.call("rbind", rep(list(st_label[[1]]), round(N2/N1) + :
undefined columns selected
Calls: Convert_Data -> data_process -> [ -> [.data.frame
Execution halted

My guess is that line 110 in R_utils.R may be changed from 1 to 2?
(Changed st_labels[[1]] to st_label[[1]] and [1:N2] to [1:N2,])

1. label.list2 <- do.call("rbind", rep(list(st_labels[[1]]), round(N2/N1)+1))[1:N2]
2. label.list2 <- do.call("rbind", rep(list(st_label[[1]]), round(N2/N1)+1))[1:N2,]

Thanks!

[bsungwoo]

When I changed the line 110 in R_utils.R as above, I crossed with another error.

[1] "Generation of 1000 test spots took 0.2 mins"
[1] "output consists of a list with two dataframes, this first one has the weighted count matrix and the second has the metadata for each spot"
Error in label.list[[i]] : subscript out of bounds
Calls: Convert_Data ... eval.parent -> eval -> eval -> write.table -> is.data.frame
Execution halted

Is it possibly related to "label.list[[i]]" in line 149 in R_utils.R? I presumed that since "label.list" contains the single-cell annotation data and its length is 1, label.list[[i]] needs to be changed to st.label[[i]] defined in line 126 (From 1 to 2 below).

1. write.csv(label.list[[i]],file=paste0(inforDir,'/ST_label/ST_label_',i,'.csv'),quote=F)
2. write.csv(st.label[[i]],file=paste0(inforDir,'/ST_label/ST_label_',i,'.csv'),quote=F)

It seems that all the issues are resolved by changing line 110 and 149 as above.
Could you check on with the issues?

Thank you!

[QSong-github]

When I changed "st_labels" to "st_label" in line 110 of R_utils.R, another error message appeared in the same line.

run real data...
[1] "Generating synthetic test spots..."
|======================================================================| 100%
[1] "Generation of 1000 test spots took 0.21 mins"
[1] "output consists of a list with two dataframes, this first one has the weighted count matrix and the second has the metadata for each spot"
Error in [.data.frame(do.call("rbind", rep(list(st_label[[1]]), round(N2/N1) + :
undefined columns selected
Calls: Convert_Data -> data_process -> [ -> [.data.frame
Execution halted

My guess is that line 110 in R_utils.R may be changed from 1 to 2?
(Changed st_labels[[1]] to st_label[[1]] and [1:N2] to [1:N2,])

1. label.list2 <- do.call("rbind", rep(list(st_labels[[1]]), round(N2/N1)+1))[1:N2]
2. label.list2 <- do.call("rbind", rep(list(st_label[[1]]), round(N2/N1)+1))[1:N2,]

Thanks!

It should be correct if changing "st_labels" to "st_label" in line 110 of R_utils.R. I will verify and modify it. However, I am not sure about the other errors that you mentioned. I will check on my side or can you share me your toy data that I can check?