abundance.lineplot {LipidomicsR}

Plot Abundance Data

Description

This function generates line plots for abundance data.

Usage

abundance.lineplot(
  data.summary,
  by = data.frame(group = c(), variable.1 = c(), variable.2 = c()),
  .width = 0.5,
  .position_dodge = 0,
  errorbar.width = 0.5,
  .xlab = "group",
  .ylab = "abundance",
  axis.title.size = 10,
  axis.title.x.vjust = 0,
  axis.title.y.vjust = 0,
  axis.text.size = 10,
  axis.line.size = 0.5,
  axis.tick.length = 0.2,
  legend.title = "",
  legend.color = "Set2",
  color.style = "Nature",
  .legend.direction = "vertical",
  .legend.position = "right",
  main.size = 10
)

Arguments

data.summary

A data frame containing summarized abundance data.

by

A data frame specifying additional variables for grouping and plotting (default is an empty data frame).

.width

The width of lines in the plot (default is 0.5).

.position_dodge

The position adjustment parameter for dodging lines (default is 0.5).

errorbar.width

The width of error bars (default is 0.5).

.xlab

The label for the x-axis (default is 'group').

.ylab

The label for the y-axis (default is 'abundance').

axis.title.size

The size of axis title text (default is 10).

axis.title.x.vjust

The vertical adjustment parameter for x-axis title (default is 0).

axis.title.y.vjust

The vertical adjustment parameter for y-axis title (default is 0).

axis.text.size

The size of axis text (default is 10).

axis.line.size

The size of axis lines (default is 0.5).

axis.tick.length

The length of axis ticks (default is 0.2).

legend.title

The title for the legend (default is an empty string).

legend.color

The color palette for the legend (default is a set of predefined colors).

color.style

The style of colors, which can be "Nature", "Science", "Lancet", "JCO", "D3", "IGV", "Star Trek", "Tron Legacy", "Rick and Morty", and "The Simpsons". Default value is "Nature".

.legend.direction

The direction of the legend ('horizontal' or 'vertical', default is 'vertical').

.legend.position

The position of the legend ('top', 'bottom', 'left', 'right', or NULL, default is 'right').

main.size

The size of plot titles (default is 10).

Value

A list of ggplot objects, each representing a line plot for abundance data of a species. In addition, the list includes a line plot for the sum of abundance of each class of lipid type, unsaturation, and carbon number.