plotInteractions: Plot group interactions

In MarcElosua/SPOTlight: `SPOTlight`: Spatial Transcriptomics Deconvolution

Plot group interactions

Description

This function takes in a matrix with the predicted proportions for each spot and returns a heatmap which = plotHeatmap or a network graph which = plotNetwork to show which cells are interacting spatially.

Usage

plotInteractions(
  x,
  which = c("heatmap", "network"),
  metric = c("prop", "jaccard"),
  min_prop = 0,
  ...
)

Arguments

x	numeric matrix with rows = samples and columns = groups. Must have at least one row and column, and at least two columns.
which	character string specifying the type of visualization: one of "heatmap" or "network".
metric	character string specifying which metric to show: one of "prop" or "jaccard".
min_prop	scalar specifying the value above which a group is considered to be contributing to a given sample. An interaction between groups i and j is counted for sample s only when both x[s, i] and x[s, j] fall above min_prop.
...	additional graphical parameters passed to plot.igraph when which = "network" (see ?igraph.plotting).

Value

base R plot

Author(s)

Marc Elosua Bayes & Helena L Crowell

Examples

library(ggplot2)
mat <- replicate(8, rnorm(100, runif(1, -1, 1)))
# Basic example
plotInteractions(mat)

### heatmap ###
# This returns a ggplot object that can be modified as such
plotInteractions(mat, which = "heatmap") +
    scale_fill_gradient(low = "#f2e552", high = "#850000") +
    labs(title = "Interaction heatmap", fill = "proportion")
        
### Network ###
# specify node names
nms <- letters[seq_len(ncol(mat))]
plotInteractions(mat, which = "network", vertex.label = nms)

# or set column names instead
colnames(mat) <- nms
plotInteractions(mat, which = "network")

# pass additional graphical parameters for aesthetics
plotInteractions(mat,
    which = "network",
    edge.color = "cyan",
    vertex.color = "pink",
    vertex.label.font = 2,
    vertex.label.color = "maroon")

MarcElosua/SPOTlight documentation built on March 7, 2024, 4:58 p.m.