Issue with count touching cells

[Athanasios72]

Hi Kent,

I have been having an issue with count_touching_cells. I have used the following code in RStudio on a Windows PC:
**base_path <- '~/OPAL R ANALYSIS/T panel/SPATIAL ANALYSIS/TOUCH PAIRS/IMminGC/SEGNO/'
paths <- list_cell_seg_files(base_path)
files <- list_cell_seg_files(base_path)

pairs <- list(
c('CD3DN', 'AE1AE3'),
c('CD3DN', 'CD3CD4'),
c('CD3DN', 'CD3CD4FOXP3'),
c('CD3DN', 'CD3CD8')
)
write_images <- FALSE
touch_counts <- purrr::map_df(files, function(path) {
count_touching_cells(path, pairs, write_images=write_images)
})**

I get the following error message:
Error in touch_pairs[, 1] : incorrect number of dimensions
Called from: unique(touch_pairs[, 1])

Is there anything wrong with the script?

Many thanks.

Kind regards,

Athanasios

[AB-Kent]

Your code looks fine. Are you using the latest version of phenoptr? If so, can you send me the cell seg data and segmentation map files that are failing? (Add cat(path, '\n') before count_touching_cells to see which one is failing; see my profile for email.)

[Athanasios72]

Thank you for your suggestion. I found the error causing file pair and removed it. The script run fine after that.

[AB-Kent]

This problem occurred when there was a single touching cell pair. Fixed with the above commit.

[AB-Kent]

Thank you for the failing example. The error occurred when there was exactly one touching cell pair. It is fixed now in the development version of phenoptr. You can install this with devtools::install_github('akoyabio/phenoptr@9000') Thanks again, Kent

…

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-- *Kent Johnson | Principal Software Developer*