save_subject_line_plots: Save line plots with mean

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

Save line plots with mean

Description

Plots the change in the feature abundances as a function of e.g. time. A line is drawn for each subject and a mean line is added. A separate plot is drawn and saved for each feature.

Usage

save_subject_line_plots(
  object,
  all_features = FALSE,
  save = TRUE,
  file_path = NULL,
  format = "emf",
  x = time_col(object),
  id = subject_col(object),
  title = "Feature_ID",
  subtitle = NULL,
  color = NA,
  color_scale = getOption("notame.color_scale_dis"),
  facet = NULL,
  text_base_size = 14,
  line_width = 0.3,
  mean_line_width = 1.2,
  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.
save	logical, if false, the plots are not saved but returned as a list
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
id	character, name of the column containing subject IDs
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
color	character, the column name to color the lines by (optional)
color_scale	the color scale as returned by a ggplot function
facet	character, the column name to facet by (optional, usually same as color)
text_base_size	integer, base size for text in figures
line_width	numeric, width of the lines
mean_line_width	numeric, width of the mean line
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

Examples

## Not run: 
save_subject_line_plots(drop_qcs(example_set),
  file_path = "./subject_line_plots.pdf",
  format = "pdf"
)

## End(Not run)
# Plot one feature
save_subject_line_plots(drop_qcs(example_set[1, ]), save = FALSE)

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