Edit the image with img_edit() then update the imgData().
img_update(
spe,
sampleid,
image_id = "lowres",
new_image_id = paste0("edited_", image_id),
overwrite = FALSE,
...
)Defaults to the output of
fetch_data(type = 'spe'). This is a
SpatialExperiment-class
object with the spot-level Visium data and information required for
visualizing the histology. See fetch_data() for more details.
A character(1) specifying which sample to plot from
colData(spe)$sample_id (formerly colData(spe)$sample_name).
A character(1) with the name of the image ID you want to
use in the background.
A character(1) specifying the new image_id to use.
A logical(1) specifying whether to overwrite the
image_id if it already exists.
Parameters passed to img_edit().
A
SpatialExperiment-class object
with an updated imgData() slot.
Other Image editing functions:
img_edit(),
img_update_all()
if (enough_ram()) {
## Obtain the necessary data
if (!exists("spe")) spe <- fetch_data("spe")
## Reduce brightness to 25% and update the imgData()
imgData(img_update(spe, sampleid = "151507", brightness = 25))
}
#> 2024-04-19 19:43:36.687831 loading file /github/home/.cache/R/BiocFileCache/c9922e59250_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> DataFrame with 13 rows and 4 columns
#> sample_id image_id data scaleFactor
#> <character> <character> <list> <numeric>
#> 1 151507 lowres #### 0.0450045
#> 2 151508 lowres #### 0.0450045
#> 3 151509 lowres #### 0.0450045
#> 4 151510 lowres #### 0.0450045
#> 5 151669 lowres #### 0.0450045
#> ... ... ... ... ...
#> 9 151673 lowres #### 0.0450045
#> 10 151674 lowres #### 0.0450045
#> 11 151675 lowres #### 0.0450045
#> 12 151676 lowres #### 0.0450045
#> 13 151507 edited_lowres #### 0.0450045