Hello,
I constructed a SpatialExperiment where spe$sample_id was a factor, which did not throw errors, and felt intuitive, given that there were a lot of columns (spots) in my data with only a handful of possible sample IDs. However, this causes problems in various internal functions, where sample ID is assumed to be character (at least this code). This leads to difficult-to-understand errors when performing normal operations on the SpatialExperiment. Perhaps either factors should be supported or errors should be thrown when attempting to set spe$sample_id to a factor.
Here's a reproducible example creating the error:
n <- length(z <- letters)
y <- list(counts = matrix(0, nrow = n, ncol = n))
cd <- DataFrame(a = seq(n), x = seq(n), y = seq(n), z)
spe1 <- SpatialExperiment(
assay = y,
colData = cd,
spatialCoordsNames = c("x", "y")
)
url <- "https://i.redd.it/3pw5uah7xo041.jpg"
spe1 <- addImg(
spe1,
sample_id = "sample01",
image_id = "pomeranian",
imageSource = url,
scaleFactor = NA_real_,
load = TRUE
)
# Works fine, because spe1$sample_id is a character vector
getImg(spe1, sample_id = spe1$sample_id[1], image_id = "pomeranian")
# Fails with difficult-to-understand error when spe1$sample_id is a factor
# of characters
spe1$sample_id = factor(spe1$sample_id)
getImg(spe1, sample_id = spe1$sample_id[1], image_id = "pomeranian")
The error message is Error in .get_img_idx(x, sample_id, image_id) : object 'sid' not found, again because the if statement here doesn't handle factors, leading to sid being undefined here.
I actually first encountered the error when trying to use spatialLIBD::vis_gene() ( I understand that getImg() is not going to be frequently called directly-- it just provokes the error most directly).
Best,
-Nick
Hello,
I constructed a
SpatialExperimentwherespe$sample_idwas a factor, which did not throw errors, and felt intuitive, given that there were a lot of columns (spots) in my data with only a handful of possible sample IDs. However, this causes problems in various internal functions, where sample ID is assumed to be character (at least this code). This leads to difficult-to-understand errors when performing normal operations on theSpatialExperiment. Perhaps either factors should be supported or errors should be thrown when attempting to setspe$sample_idto a factor.Here's a reproducible example creating the error:
The error message is
Error in .get_img_idx(x, sample_id, image_id) : object 'sid' not found, again because the if statement here doesn't handle factors, leading tosidbeing undefined here.I actually first encountered the error when trying to use
spatialLIBD::vis_gene()( I understand thatgetImg()is not going to be frequently called directly-- it just provokes the error most directly).Best,
-Nick