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lines changed Original file line number Diff line number Diff line change 33# ' This function visualizes the histology image for selected sample. Matches
44# ' crop and settings of [vis_clus()] and [vis_gene()].
55# '
6- # ' @param spe A
7- # ' [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class]
8- # ' object. See [fetch_data()] for how to download some example objects or
9- # ' [read10xVisiumWrapper()] to read in `spaceranger --count` output files and
10- # ' build your own `spe` object.
11- # ' @param sampleid A `character(1)` specifying which sample to plot from
12- # ' `colData(spe)$sample_id` (formerly `colData(spe)$sample_name`).
13- # ' @param image_id A `character(1)` with the name of the image ID you want to
14- # ' use in the background.
15- # ' @param is_stitched A \code{logical(1)} vector: If `TRUE`, expects a
16- # ' [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class] built
17- # ' with `visiumStitched::build_spe()`.
18- # ' <http://research.libd.org/visiumStitched/reference/build_spe.html>; in
19- # ' particular, expects a logical colData column `exclude_overlapping`
20- # ' specifying which spots to exclude from the plot. Sets `auto_crop = FALSE`.
6+ # ' @inheritParams vis_clus
217# ' @param title_suffix A `character(1)` passed to [paste()][base::paste] to
228# ' modify the title of the plot following the `sampleid`.
239# '
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