save_group_lineplots: Save line plots with errorbars by group

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

Plots the change in the feature abundances as a function of e.g. time. A line is drawn for each group and error bars are added. A separate plot is drawn for each feature.

Usage

save_group_lineplots(object, all_features = FALSE, file, width = 8,
  height = 6, x = time_col(object), group = group_col(object),
  fun.data = "mean_cl_boot", fun.y = NULL, fun.ymin = NULL,
  fun.ymax = NULL, position_dodge_amount = 0.2, color_scale = NULL)

Arguments

object	a MetaboSet object
all_features	logical, should all features be used? If FALSE (the default), flagged features are removed before visualization.
file	path to the PDF file where the plots should be saved
width, height	width and height of the plots in inches
x	character, name of the column to be used as x-axis
group	character, name of the column containing group information, used for coloring
fun.data	passed to ggplot2::stat_summary and used for errorbars, "A function that is given the complete data and should return a data frame with variables ymin, y, and ymax."
fun.ymin, fun.y, fun.ymax	Alternative to fun.data, passed to ggplot2::stat_summary, "supply three individual functions that are each passed a vector of x's and should return a single number"
color_scale	the color scale as returned by a ggplot function
position_dodge_amout	numeric: how much the group mean points should dodge away from each other

See Also

stat_summary

Examples

## Not run: save_group_lineplots(drop_qcs(merged_sample), file = "group_lineplots.pdf")

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.