A compact gene-filtered version of a human pancreatic intraepithelial
neoplasia (PanIN) 10x Visium dataset from GSE254829. The object keeps the
1986 non-background tissue spots from sample GSM8058244 (PanIN-LG2), with a
Spatial assay, a slice1 Visium image, and tissue coordinates in metadata
columns x and y. Metadata column coda_label stores the dominant CODA
microanatomical component for each spot, and coda_score stores its
percentage. Component percentage columns are stored with the coda_ prefix,
and the matched CODA table is stored in @tools$GSE254829_coda_table. To
keep the package data small and directly usable with the bundled panc8_sub
reference, the object retains the top 5000 genes shared with panc8_sub,
ranked by total spatial counts.
Source
Derived from the GSE254829 human PanIN 10x
Visium dataset:
GSE254829.
The package object uses the GEO supplementary files
GSM8058244_PanIN-LG2.tar.gz and
GSE254829_codatable_may202024.csv.gz.
Examples
data(visium_human_pancreas_sub)
SeuratObject::Images(visium_human_pancreas_sub)
#> [1] "slice1"
head(visium_human_pancreas_sub@meta.data[, c("x", "y")])
#> x y
#> TGGTATCGGTCTGTAT-1 3859 662
#> ATTATCTCGACAGATC-1 3914 662
#> TGAGATCAAATACTCA-1 3969 662
#> CTGGTCCTAACTTGGC-1 4024 662
#> ATAGTCTTTGACGTGC-1 4079 662
#> GGGTGGTCCAGCCTGT-1 4134 662
SpatialSpotPlot(visium_human_pancreas_sub, group.by = "coda_label")
