spaceranger 2.0 renamed tissue_positions_list.csv to tissue_positions.csv

[simoncmo]

Hi Seurat team,

For the latest spaceranger 2.0 pipeline, 10x renamed the output tissue_positions_list.csv to tissue_positions.csv

Load10X_spatial failed at Read10X_Image

# insert reproducible example here
Load10X_spatial(SEURAT_OUTPUT_PATH)

Error in file(file, "rt") : cannot open the connection
6.
read.csv(file = file.path(image.dir, "tissue_positions_list.csv"),
col.names = c("barcodes", "tissue", "row", "col", "imagerow",
"imagecol"), header = FALSE, as.is = TRUE, row.names = 1)
5.
Read10X_Image(image.dir = file.path(data.dir, "spatial"), filter.matrix = filter.matrix)

At the moment I'm seeing this file name being hardcoded in preprocessing.R without a parameter to set it

Read10X_Image <- function(image.dir, image.name = "tissue_lowres_image.png", filter.matrix = TRUE, ...) {
  image <- readPNG(source = file.path(image.dir, image.name))
  scale.factors <- fromJSON(txt = file.path(image.dir, 'scalefactors_json.json'))
  tissue.positions <- read.csv(
    file = file.path(image.dir, 'tissue_positions_list.csv'),
    col.names = c('barcodes', 'tissue', 'row', 'col', 'imagerow', 'imagecol'),
    header = FALSE,
    as.is = TRUE,
    row.names = 1
  )

Could you please add an official fix to this function to make it compatible with both file names?
Thanks!!

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. Have you tried the dev branch? There was PR from 10X team couple months ago to address this.

#6208 (comment)

Best,
Sam