findVisiumHDGraph error

[julienmortier]

Whenever I attempt to use findVisiumHDGraph on Visium HD Space Ranger output data, I get an error (see below). I have already tried multiple datasets and resolutions and a couple of different setting for the parameters, but I keep getting the same error. I'm not sure whether this is user error or a bug in the function. I get the same error if I try to calculate the spatial graph directly in readVisiumHD() (add_graph = TRUE). Any ideas on what is causing the issue?

data_dir <- "E:/Visium_HD/SVT001-008-test/spaceranger_output/SVT005/outs/binned_outputs"

sfe <- readVisiumHD(
  data_dir = data_dir,
  bin_size = 16,
  sample_id = NULL,
  type = "sparse",
  data = "filtered",
  images = c("lowres", "hires"),
  unit = "full_res_image_pixel",
  style = "W",
  zero.policy = TRUE,
  row.names = "symbol",
  add_graph = FALSE,
  flip = "image",
)

colGraph(sfe, "visiumHD") <- findVisiumHDGraph(sfe)

Error in apply(gm, 1, function(x) x[!is.na(x)]) : 
  dim(X) must have a positive length