Plot Feature Prevalence from Carrier Summaries — plot.feature.prevalence • gflow

Visualize prevalence proportions computed by count.feature.carriers() or basin.feature.carriers(). The input carriers.df must have columns k and p, with feature names in rownames(carriers.df).

The function can use either base R graphics or ggplot2, controlled by use.ggplot. Features can be restricted to the top top.m by prevalence or filtered by min.p.

Usage

# S3 method for class 'feature.prevalence'
plot(
  x,
  top.m = NULL,
  min.p = NULL,
  sort.by = c("p", "k"),
  decreasing = TRUE,
  use.ggplot = FALSE,
  plot.type = c("lollipop", "bar", "dot"),
  title = NULL,
  xlab = NULL,
  show.values = FALSE,
  cex.labels = 0.8,
  stick.col = "grey30",
  point.col = "black",
  bar.fill = "grey70",
  label.col = "black",
  label.font = 1,
  label.face = c("plain", "bold", "italic", "bold.italic"),
  ...
)

Arguments

x: A data.frame with columns k (integer) and p (numeric in \([0,1]\)) and row names corresponding to feature/phylotype names.
top.m: Optional integer; if provided, plot only the top.m most prevalent features by p.
min.p: Optional numeric in \([0,1]\); if provided, plot only features with p >= min.p. Applied after top.m if both are provided.
sort.by: Character string specifying sort key. One of "p" (default) or "k".
decreasing: Logical; if TRUE (default), sort decreasing.
use.ggplot: Logical; if TRUE use ggplot2 (requires ggplot2 installed), otherwise use base R graphics.
plot.type: Character string; one of "lollipop" (default), "bar", or "dot".
title: Optional plot title.
xlab: Optional x-axis label.
show.values: Logical; if TRUE, annotate prevalence values on the plot (ggplot2 only).
cex.labels: Numeric; base R only, label size for y-axis feature names.
stick.col: Color for stick/segment lines (lollipop only). Default "grey30".
point.col: Color for points (lollipop and dot). Default "black".
bar.fill: Fill color for bars (bar plot only). Default "grey70".
label.col: Color for feature (y-axis) labels. Default "black".
label.font: Base R only: font for y-axis labels (1=plain, 2=bold, 3=italic, 4=bold.italic). Default 1.
label.face: ggplot2 only: face for y-axis labels. One of "plain", "bold", "italic", "bold.italic". Default "plain".
...: Additional arguments passed to base plotting functions (base R) or ignored (ggplot2) except where supported.

Value

Invisibly returns the (possibly filtered/reordered) data.frame used for plotting. If use.ggplot=TRUE, also returns the ggplot object as attribute "plot".