save_dc_plots: Drift correction plots

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

Drift correction plots

Description

Plots the data before and after drift correction, with the regression line drawn with the original data. If the drift correction was done on log-transformed data, then plots of both the original and log-transformed data before and after correction are drawn. The plot shows 2 standard deviation spread for both QC samples and regular samples.

Usage

save_dc_plots(
  orig,
  dc,
  predicted,
  file,
  log_transform = TRUE,
  width = 16,
  height = 8,
  color = "QC",
  shape = color,
  color_scale = getOption("notame.color_scale_dis"),
  shape_scale = scale_shape_manual(values = c(15, 16))
)

Arguments

orig	a MetaboSet object, before drift correction
dc	a MetaboSet object, after drift correction as returned by correct_drift
predicted	a matrix of predicted values, as returned by dc_cubic_spline
file	path to the PDF file where the plots should be saved
log_transform	logical, was the drift correction done on log-transformed data?
width, height	width and height of the plots in inches
color	character, name of the column used for coloring the points
shape	character, name of the column used for shape
color_scale	the color scale as returned by a ggplot function
shape_scale	the shape scale as returned by a ggplot function

Details

If shape is set to NULL (the default), the column used for color is also used for shape

See Also

correct_drift, inspect_dc

Examples

## Not run: 
dc <- dc_cubic_spline(merged_sample)
corrected <- dc$object
inspected <- inspect_dc(
  orig = merged_sample, dc = corrected,
  check_quality = TRUE
)
save_dc_plots(
  orig = merged_sample, dc = corrected, predicted = dc$predicted,
  file = "drift_plots.pdf"
)

## End(Not run)

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