Plot average gene expression along spatial distance

Visualizes how the average expression of specified genes varies along a spatial distance gradient. The spatial distance is binned, and the average expression within each bin is plotted as a heatmap.

Usage

plotSpatialExpression(
  exp_mat = NULL,
  spatial_distance = NULL,
  genes = NULL,
  n_bins = 50,
  scale_method = c("none", "zscore", "minmax"),
  n_labels = 6,
  row_gap = 0.1,
  column_gap = 0,
  label_x = "Spatial distance",
  label_y = "Gene",
  theme_ggplot = theme_spneigh()
)

Arguments

exp_mat

A normalized gene expression matrix (genes x cells), either a matrix or dgCMatrix. Typically log-normalized counts, e.g., from a Seurat object.

spatial_distance

A named numeric vector containing the spatial distance (or weights) for each cell.

genes

Character vector specifying gene names to be plotted. Must match row names in exp_mat.

n_bins

Integer. Number of bins to divide the spatial distance into. Default is 50.

scale_method

A string indicating how to scale the average expression values across bins for each gene. Options are:

"none"

No scaling (default). The average expression is plotted as-is.

"zscore"

Standardize expression (mean 0, SD 1) per gene using scale().

"minmax"

Normalize expression to [0, 1] range per gene using scales::rescale().

n_labels

Integer. Number of axis labels to show along the distance axis. Default is 6.

row_gap

Numeric between 0 (inclusive) and 1 (exclusive). Gap between rows (genes) in the plot. Default is 0.1.

column_gap

Numeric between 0 (inclusive) and 1 (exclusive). Gap between columns (distance bins) in the plot. Default is 0.

label_x

Character. Label for the x-axis. Default is "Spatial distance".

label_y

Character. Label for the y-axis. Default is "Gene".

theme_ggplot

A ggplot2 theme object. Default is theme_spneigh().

Value

A ggplot2 object displaying a heatmap of binned average gene expression across spatial distances.

Examples

# Example spatial expression heatmap
set.seed(1)
exp_mat <- matrix(runif(1000), nrow = 10)
rownames(exp_mat) <- paste0("Gene", 1:10)
spatial_distance <- runif(100)
plotSpatialExpression(
    exp_mat = exp_mat,
    spatial_distance = spatial_distance,
    genes = rownames(exp_mat)[1:5]
)