save_scatter_plots: Save scatter plots of each feature against a set variable

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

Save scatter plots of each feature against a set variable

Description

Draws a scatterplots with a feature on y-axis and another variable on x-axis. A separate plot is drawn and saved for each feature.

Usage

save_scatter_plots(
  object,
  x = "Injection_order",
  save = TRUE,
  file_path = NULL,
  format = "emf",
  all_features = FALSE,
  color = NULL,
  color_scale = NA,
  shape = NULL,
  title = "Feature_ID",
  subtitle = NULL,
  shape_scale = getOption("notame.shape_scale"),
  text_base_size = 14,
  point_size = 2,
  title_line_length = 40,
  theme = theme_bw(base_size = text_base_size),
  ...
)

Arguments

object	a MetaboSet object
x	character, name of the column to be used as x-axis
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
all_features	logical, should all features be used? If FALSE (the default), flagged features are removed before visualization.
color	character, name of the column to be used for coloring
color_scale	the color scale as returned by a ggplot function. Set to NA to choose the appropriate scale based on the class of the coloring variable.
shape	character, name of the column used for shape
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
shape_scale	the shape scale as returned by a ggplot function
text_base_size	integer, base size for text in figures
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

Examples

## Not run: 
# Against injection order, colored by group
save_scatter_plots(
  object = merged_sample[1:10],
  x = "Injection_order",
  color = "Group",
  file_path = "./scatter_plots.pdf",
  format = "pdf"
)

## End(Not run)
# Plot one feature
save_scatter_plots(merged_sample[5, ], save = FALSE, color = "Group")

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