Save scatter plots of each feature against a set variable

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),
  assay.type = NULL,
  ...
)

Arguments

object

a SummarizedExperiment or MetaboSet object

x

character, name of the column to be used as x-axis

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

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 feature data 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 str_wrap

theme

a ggplot theme to be added to the plot

assay.type

character, assay to be used in case of multiple assays

...

other arguments to graphic device functions, like width and height

Value

By default, the function is invoked for its plot-saving side effect. The function returns a list of plots when save = FALSE.

See also

save_plot

Examples

data(example_set)
# Against injection order, colored by group
save_scatter_plots(
  object = example_set[1:10],
  x = "Injection_order",
  color = "Group",
  file_path = "./scatter_plots.pdf",
  format = "pdf"
)
#> INFO [2025-06-23 22:38:29] Saved scatter plots to: ./scatter_plots.pdf
# Plot one feature
save_scatter_plots(example_set[1, ], save = FALSE)
#> Just a remainder, creating a long list of plots takes a lot of memory!
#> [[1]]

#>