save_beeswarm_plots: Save beeswarm plots of each feature by group

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

Save beeswarm plots of each feature by group

Description

Draws a beeswarm plot of feature abundances in each group. A separate plot is drawn and saved for each feature.

Usage

save_beeswarm_plots(
  object,
  all_features = FALSE,
  save = TRUE,
  file_path = NULL,
  format = "emf",
  x = group_col(object),
  add_boxplots = FALSE,
  title = "Feature_ID",
  subtitle = NULL,
  color = group_col(object),
  color_scale = getOption("notame.color_scale_dis"),
  text_base_size = 14,
  cex = 2,
  size = 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.
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
add_boxplots	logical, should boxplots be added to the figure?
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, name of the column to be used for coloring
color_scale	the color scale as returned by a ggplot function
text_base_size	integer, base size for text in figures
cex	numeric, scaling for adjusting point spacing
size	numeric, size of 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

Examples

## Not run: 
# Default beeswarms by group
save_beeswarm_plots(drop_qcs(merged_sample),
  file_path = "./beeswarm_plots.pdf",
  format = "pdf"
)
# x and color can be a different variable
save_beeswarm_plots(drop_qcs(merged_sample)[1:10],
  file_path = "./beeswarm_plots/",
  format = "png",
  x = "Time",
  color = "Group"
)

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

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