plotSpots: plotSpots

In lmweber/ggspavis: Visualization functions for spatial transcriptomics data

plotSpots

Description

Plotting functions for spatial transcriptomics data.

Usage

plotSpots(
  spe,
  x_coord = NULL,
  y_coord = NULL,
  sample_id = NULL,
  in_tissue = "in_tissue",
  annotate = NULL,
  feature_names = NULL,
  assay_name = "counts",
  pal = NULL,
  point_size = 0.3,
  legend_position = "right",
  legend_point_size = 3,
  show_axes = FALSE,
  y_reverse = TRUE,
  text_by = NULL,
  text_by_size = 5,
  text_by_color = "black"
)

Arguments

spe	Input data, assumed to be a SpatialExperiment or SingleCellExperiment object.
x_coord	Name of column in spatialCoords (for a SpatialExperiment input object) or colData (for a SingleCellExperiment input object) containing x coordinates. Default = NULL (for a SpatialExperiment, the first column of spatialCoords will be selected in this case).
y_coord	Name of column in spatialCoords (for a SpatialExperiment input object) or colData (for a SingleCellExperiment input object) containing y coordinates. Default = NULL (for a SpatialExperiment, the second column of spatialCoords will be selected in this case).
sample_id	Name of column in colData containing sample IDs. This argument is only required for datasets containing multiple samples (tissue sections). If provided, samples will be shown in multiple panels using facetting. Default = NULL.
in_tissue	Name of column in colData identifying spots over tissue (e.g. "in_tissue" for 10x Genomics Visium datasets). If this argument is provided, only spots over tissue will be shown. Default = "in_tissue". Set to NULL to display all spots.
annotate	Variable to show as annotations. This may be discrete or continuous. For a discrete variable (e.g. cluster labels), this should be the name of a column in colData containing a character vector or factor. For a continuous variable (e.g. a gene name), this should be an entry in feature_names. Default = NULL.
feature_names	Name of column in rowData containing names of continuous features to plot (e.g. gene names). For example, set to feature_names = "gene_name" if gene names are stored in a column named "gene_name". This argument is used if annotate is a continuous variable. Default = NULL, in which case the row names of the input object will be used.
assay_name	Name of assay in input object containing values to plot for a continuous variable. Default = "counts".
pal	Color palette for annotations. Options for discrete values are "libd_layer_colors", "Okabe-Ito", or any vector of color names or hex values. For continuous values, provide a vector of length 2 for the low and high range, e.g. c("gray90", "navy").
point_size	Point size. Default = 0.3.
legend_position	Legend position for discrete annotations. Options are "left", "right", "top", "bottom", and "none". Default = "right".
legend_point_size	Legend point size for discrete annotations. Default = 3.
show_axes	Whether to show axis titles, text, and ticks. Default = FALSE.
y_reverse	Whether to reverse y coordinates. This is usually required for 10x Genomics Visium datasets when using the default coordinate values. Default = TRUE. Set to FALSE if not needed, e.g. for other platforms.
text_by	Column name of annotation labels to display over each cluster of points. This will usually be the same as annotate. Alternatively, another column may be used (e.g. with more readable classes or shorter strings). Only used for discrete annotate. Default = NULL.
text_by_size	Text size for annotation labels over each cluster. Default = 5.
text_by_color	Color name or hex code for annotation labels. Default = "black".

Details

Function to create spot plot showing spatial locations in x-y coordinates with optional annotations such as cluster labels, expression of a gene, or quality control metrics.

Value

Returns a ggplot object, which may be further modified using ggplot functions.

Author(s)

Lukas M. Weber and Yixing E. Dong

Examples

library(STexampleData)

# discrete annotations
spe <- Visium_humanDLPFC()
plotSpots(spe, annotate = "ground_truth")

# continuous annotations
spe <- Visium_mouseCoronal()
plotSpots(spe, annotate = "Gapdh", feature_names = "gene_name")

lmweber/ggspavis documentation built on April 4, 2024, 3:21 a.m.