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Plot m/z vs retention time plot (cloud plot)

Source: R/scatter.R
mz_rt_plot.Rd

Plots a scatter plot of results of statistical tests, where each point represents a feature. The plot has retention time on x-axis, m/z on y-axis and the size of the points is scaled based on p-value

Usage

mz_rt_plot(
  object,
  p_col = NULL,
  p_limit = NULL,
  mz_col = NULL,
  rt_col = NULL,
  color = NULL,
  title = "m/z retention time",
  subtitle = NULL,
  color_scale = getOption("notame.color_scale_con"),
  ...
)

# S4 method for class 'MetaboSet'
mz_rt_plot(
  object,
  p_col = NULL,
  p_limit = NULL,
  mz_col = NULL,
  rt_col = NULL,
  color = NULL,
  title = "m/z vs retention time",
  subtitle = NULL,
  color_scale = getOption("notame.color_scale_con"),
  all_features = FALSE
)

# S4 method for class 'data.frame'
mz_rt_plot(
  object,
  p_col = NULL,
  p_limit = NULL,
  mz_col = NULL,
  rt_col = NULL,
  color = NULL,
  title = "m/z vs retention time",
  subtitle = NULL,
  color_scale = getOption("notame.color_scale_con")
)

# S4 method for class 'SummarizedExperiment'
mz_rt_plot(
  object,
  p_col = NULL,
  p_limit = NULL,
  mz_col = NULL,
  rt_col = NULL,
  color = NULL,
  title = "m/z vs retention time",
  subtitle = NULL,
  color_scale = getOption("notame.color_scale_con"),
  all_features = FALSE
)

Arguments

object

a SummarizedExperiment , MetaboSet object or a data frame. Feature data is used. If x is a data frame, it is used as is.

p_col

the column name containing p-values. This is used to scale the size of the points.

p_limit

numeric, limits plotted features by p-values. If NULL, plots all features.

mz_col, rt_col

the column names for m/z and retention time. If NULL, automatic detection is attempted.

color

the column name used to color the points

title

The plot title

subtitle

The plot subtitle

color_scale

color scale as returned by a ggplot function. Defaults to current continuous color scale.

...

parameters passed to geom_point, such as shape and alpha values. New aesthetics can also be passed using mapping = aes(...).

all_features

logical, should all features be retained? Should be used only if x is a SummarizedExperiment object.

Value

A ggplot object.

Examples

data(example_set)
# Compute results from a linear model
lm_results <- perform_lm(example_set, formula_char = "Feature ~ Group")
#> INFO [2025-06-23 22:36:59] Starting linear regression.
#> INFO [2025-06-23 22:37:00] Linear regression performed.
with_results <- join_rowData(example_set, lm_results)

# Plot from the SummarizedExperiment object
# automatically facet by analytical mode in variable Split
mz_rt_plot(with_results, p_col = "GroupB_P", color = "GroupB_Estimate")
#> INFO [2025-06-23 22:37:00] Identified m/z column Average_Mz and retention time column Average_Rt_min
#> Multiple splits detected, plotting them to separate panes.


# Plot the results from the results dataframe
lm_data <- dplyr::left_join(as.data.frame(rowData(example_set)), lm_results)
#> Joining with `by = join_by(Feature_ID)`
mz_rt_plot(lm_data, p_col = "GroupB_P", color = "GroupB_Estimate")
#> INFO [2025-06-23 22:37:00] Identified m/z column Average_Mz and retention time column Average_Rt_min
#> Multiple splits detected, plotting them to separate panes.