Plot group interactions

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"), 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".

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

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")
#> Scale for 'fill' is already present. Adding another scale for 'fill', which
#> will replace the existing scale.

        
### 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")