save_group_lineplots: Save line plots with errorbars by group

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

Save line plots with errorbars by group

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,
  save = TRUE,
  file_path = NULL,
  format = "emf",
  x = time_col(object),
  group = group_col(object),
  title = "Feature_ID",
  subtitle = NULL,
  fun.data = "mean_cl_boot",
  fun = NULL,
  fun.min = NULL,
  fun.max = NULL,
  position_dodge_amount = 0.2,
  color_scale = getOption("notame.color_scale_dis"),
  text_base_size = 14,
  line_width = 0.5,
  point_size = 4,
  title_line_length = 40,
  theme = theme_bw(base_size = text_base_size),
  ...
)

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	character, a file path for PDF or prefix added to the file paths for other formats
format	character, format in which the plots should be saved
x	character, name of the column to be used as x-axis
group	character, name of the column containing group information, used for coloring
title, subtitle	column names from fData to use as plot title/filename and subtitle. Set to NULL for no title/subtitle, this creates running numbered filenames
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.min, fun, fun.max	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"
position_dodge_amount	numeric: how much the group mean points should dodge away from each other
color_scale	the color scale as returned by a ggplot function
text_base_size	integer, base size for text in figures
line_width	numeric, width of the lines
point_size	numeric, size of the points
title_line_length	integer, maximum length of the title line in characters, passed to stringr::str_wrap
theme	a ggplot theme to be added to the plot
...	other arguments to graphic device functions, like width and height

See Also

save_plot, stat_summary

Examples

## Not run: 
save_group_lineplots(drop_qcs(merged_sample),
  file_path = "./group_line_plots.pdf",
  format = "pdf"
)
save_group_lineplots(drop_qcs(merged_sample)[1:10],
  file_path = "./group_line_plots/",
  format = "png"
)

## End(Not run)
# Plot one feature
save_group_lineplots(drop_qcs(merged_sample[5, ]), save = FALSE)

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.