vis_clus: Sample spatial cluster visualization

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Sample spatial cluster visualization

Description

This function visualizes the clusters for one given sample at the spot-level using (by default) the histology information on the background. To visualize gene-level (or any continuous variable) use vis_gene().

Usage

vis_clus(
  spe,
  sampleid = unique(spe$sample_id)[1],
  clustervar,
  colors = c("#b2df8a", "#e41a1c", "#377eb8", "#4daf4a", "#ff7f00", "gold", "#a65628",
    "#999999", "black", "grey", "white", "purple"),
  spatial = TRUE,
  image_id = "lowres",
  alpha = NA,
  point_size = 2,
  auto_crop = TRUE,
  na_color = "#CCCCCC40",
  is_stitched = FALSE,
  ...
)

Arguments

spe	A SpatialExperiment-class object. See fetch_data() for how to download some example objects or read10xVisiumWrapper() to read in spaceranger --count output files and build your own spe object.
sampleid	A character(1) specifying which sample to plot from colData(spe)$sample_id (formerly colData(spe)$sample_name).
clustervar	A character(1) with the name of the colData(spe) column that has the cluster values.
colors	A vector of colors to use for visualizing the clusters from clustervar. If the vector has names, then those should match the values of clustervar.
spatial	A logical(1) indicating whether to include the histology layer from geom_spatial(). If you plan to use ggplotly() then it's best to set this to FALSE.
image_id	A character(1) with the name of the image ID you want to use in the background.
alpha	A numeric(1) in the ⁠[0, 1]⁠ range that specifies the transparency level of the data on the spots.
point_size	A numeric(1) specifying the size of the points. Defaults to 1.25. Some colors look better if you use 2 for instance.
auto_crop	A logical(1) indicating whether to automatically crop the image / plotting area, which is useful if the Visium capture area is not centered on the image and if the image is not a square.
na_color	A character(1) specifying a color for the NA values. If you set alpha = NA then it's best to set na_color to a color that has alpha blending already, which will make non-NA values pop up more and the NA values will show with a lighter color. This behavior is lost when alpha is set to a non-NA value.
is_stitched	A logical(1) vector: If TRUE, expects a SpatialExperiment-class built with visiumStitched::build_spe(). http://research.libd.org/visiumStitched/reference/build_spe.html; in particular, expects a logical colData column exclude_overlapping specifying which spots to exclude from the plot. Sets auto_crop = FALSE.
...	Passed to paste0() for making the title of the plot following the sampleid.

Details

This function subsets spe to the given sample and prepares the data and title for vis_clus_p().

Value

A ggplot2 object.

See Also

Other Spatial cluster visualization functions: frame_limits(), vis_clus_p(), vis_grid_clus()

Examples

if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("spe")) spe <- fetch_data("spe")

    ## Check the colors defined by Lukas M Weber
    libd_layer_colors

    ## Use the manual color palette by Lukas M Weber
    p1 <- vis_clus(
        spe = spe,
        clustervar = "layer_guess_reordered",
        sampleid = "151673",
        colors = libd_layer_colors,
        ... = " LIBD Layers"
    )
    print(p1)

    ## Without auto-cropping the image
    p2 <- vis_clus(
        spe = spe,
        clustervar = "layer_guess_reordered",
        sampleid = "151673",
        colors = libd_layer_colors,
        auto_crop = FALSE,
        ... = " LIBD Layers"
    )
    print(p2)

    ## Without histology
    p3 <- vis_clus(
        spe = spe,
        clustervar = "layer_guess_reordered",
        sampleid = "151673",
        colors = libd_layer_colors,
        ... = " LIBD Layers",
        spatial = FALSE
    )
    print(p3)

    ## With some NA values
    spe$tmp <- spe$layer_guess_reordered
    spe$tmp[spe$sample_id == "151673"][seq_len(500)] <- NA
    p4 <- vis_clus(
        spe = spe,
        clustervar = "tmp",
        sampleid = "151673",
        colors = libd_layer_colors,
        na_color = "white",
        ... = " LIBD Layers"
    )
    print(p4)
}

LieberInstitute/spatialLIBD documentation built on Dec. 19, 2024, 7:12 p.m.