Plot a Group Comparison

Two views of a compare_lsa() result. The default "barrel" is a back-to-back pyramid (one row per transition): the first group's bar runs left and the second's right, bar length is each group's transition probability, bar colour is each group's log odds ratio (blue = over-represented, red = avoided, following the vcd / mosaic convention), bar ends show the observed count, and the centre chip shows the difference p-value (bold and starred when significant). The bar of the group with the higher value gets a border that darkens with the size of the difference (faint = small, dark = large). For more than two groups, one barrel is drawn per pair via facets. The "heatmap" style draws the signed difference as a from x to grid on the same diverging scale.

Usage

# S3 method for class 'lsa_comparison'
plot(
  x,
  style = c("barrel", "heatmap"),
  value = c("prob", "count"),
  rank = c("frequency", "effect"),
  top_n = 12L,
  ...
)

# S3 method for class 'lsa_comparison_pairwise'
plot(
  x,
  style = c("barrel", "heatmap"),
  value = c("prob", "count"),
  rank = c("frequency", "effect"),
  top_n = 12L,
  ...
)

Arguments

x

An lsa_comparison or lsa_comparison_pairwise object.

style

"barrel" (default) or "heatmap".

value

For "barrel", the quantity mapped to bar length: "prob" (transition probability, default) or "count".

rank

For "barrel", how to choose which transitions to show: "frequency" (default) ranks by pooled observed count – the backbone transitions, which are mostly over-represented (blue); "effect" ranks by the strongest association in either group (|log OR|, among tested cells), surfacing both over- (blue) and under-represented / avoided (red) transitions.

top_n

For "barrel", how many transitions to show (highest rank on top; for the pairwise object the ranking is shared across facets so they line up). Default 12.

...

Reserved.

Value

A ggplot object (drawn when printed). Needs ggplot2.

See also

compare_lsa(), plot.lsa()

Examples

# \donttest{
grp <- ifelse(group_regulation$T1 == "plan", "starts_plan", "other")
g <- lsa(group_regulation, group = grp)
cmp <- compare_lsa(g, R = 200)
plot(cmp)                    # back-to-back barrel

plot(cmp, style = "heatmap") # difference heatmap

# }