mz_rt_plot: Plot m/z vs retention time plot

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

Plot m/z vs retention time plot

Description

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"),
  ...
)

Arguments

object	a MetaboSet object or a data frame. If x is a MetaboSet object, fData(x) 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.
all_features	logical, should all features be retained? Should be used only if x is a MetaboSet object.

Value

a ggplot object

Examples

# Compute results from a linear model
lm_results <- perform_lm(merged_sample, formula_char = "Feature ~ Group")
with_results <- join_fData(merged_sample, lm_results)

# Plot from the MetaboSet object
# automatically facet by analytical mode in variable Split
mz_rt_plot(with_results, p_col = "GroupB_P", color = "GroupB_Estimate")

# Plot the results from the results dataframe
mz_rt_plot(with_results, p_col = "GroupB_P", color = "GroupB_Estimate")

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