Skip to contents

Plot retention time versus chain length and saturation

Source: R/plots-qc-identification.R
plot_rt_vs_chain.Rd

Generates scatter plots of retention time (RT) versus either chain length, degree of saturation (double bonds), or equivalent carbon number (ECN) of lipid features of different feature classes. This visualization can be useful in identifying annotation (peak picking) errors in reversed-phase (RP)-LC lipidomics dataset arising from isotopic, isobaric, isomeric, or unknown interferences.

Usage

plot_rt_vs_chain(
  data = NULL,
  x_var = c("total_c", "total_db", "ecn"),
  qc_types = NA,
  outliers_highlight = TRUE,
  outlier_residual_min = 0.15,
  outlier_print = TRUE,
  ecn_k = 1.5,
  include_qualifier = FALSE,
  robust_regression = TRUE,
  cols_page = 5,
  point_size = NULL,
  point_alpha = 0.9,
  line_transparency = 0.5,
  font_base_size = NULL,
  autoscale = TRUE,
  legend_position = NULL,
  legend_size = NULL,
  show_legend_title = NULL,
  title = NULL,
  strip_text_size = NULL,
  strip_bg_color = NULL
)

Arguments

data

A MRMhubExperiment object.

x_var

Variable to use for the x-axis. One of "total_c", "total_db", or "ecn".

qc_types

A character vector specifying the QC types to plot. It must contain at least one element. The default NA plots any of the non-blank QC types ("SPL", "TQC", "BQC", "HQC", "MQC", "LQC", "NIST", "LTR") present in the dataset.

outliers_highlight

Whether to highlight potential outliers in the plot. Default is TRUE.

outlier_residual_min

Minimum value for the residuals to be considered an outlier (default is 0.15). The value corresponds to the RT difference betweem the fitted line and the median RT of the feature. The value is used to flag outliers.

outlier_print

Whether to print the features that are flagged as potential outliers to the console. Default is TRUE.

ecn_k

Constant for ECN calculation (ECN = C - ecn_k* DB), see Details. Default is 1.5.

include_qualifier

Whether to include qualifier features.

robust_regression

Whether to use robust regression, which is less sensitive to outlier (default is TRUE).

cols_page

Number of facet columns, representing different feature classes, shown per page (default is 5).

point_size

Size of the data points. Default is 2

point_alpha

Alpha transparency of the data point. Default is 0.9

line_transparency

Alpha transparency of the regression lines. Default is 0.9

font_base_size

Numeric. Base font size (in points) for plot text; all plot text scales proportionally with this value. NULL (default) uses the global default set by mrmhub_set_plot_defaults() if one is in effect, otherwise an automatic size (derived from the facet-column count on paged plots, or the per-plot default shown in the Usage section above).

autoscale

Logical. When TRUE (default), font_base_size and point_size left as NULL are sized automatically from cols_page (more facet columns per page give smaller text and points). Any value passed explicitly always takes precedence. When FALSE, unset sizes fall back to the single-plot defaults.

legend_position

Optional legend placement. One of "right", "left", "top", "bottom", "none"; a corner keyword "inside-tr", "inside-tl", "inside-br", "inside-bl"; or a numeric c(x, y) in [0, 1] coordinates. NULL (default) keeps the current placement, unless a global default is set with mrmhub_set_plot_defaults().

legend_size

Optional single multiplier of font_base_size (when <= 3) or absolute point size (when > 3) that scales the whole legend: text, title, key and the plotted symbols. NULL (default) leaves the legend unchanged.

show_legend_title

Logical. NULL (default) keeps the legend title, unless a global default is set with mrmhub_set_plot_defaults(); FALSE hides it, TRUE forces it shown.

title

Optional plot title. NULL (default) or NA shows no title; a character string is shown as the title.

strip_text_size

Optional facet strip text size, as a multiplier of font_base_size (when <= 3) or an absolute point size (when > 3). NULL (default) inherits from font_base_size.

strip_bg_color

Optional facet strip background fill colour. The strip text colour is set automatically for contrast (white on a dark fill, black on a light one). NULL (default) keeps the house dark-navy strips.

Value

A ggplot object representing faceted scatter plots

Details

The retention time can be either plotted against the total number of carbon atoms with the total number of double bonds as curves, or opposite, with the total double bond number as x axis and the total number of carbon atoms as curves. Alternatively, the retention time can be plotted against the ECN, which is calculated as \(ECN = C_{total} - ecn_k \times DB_{total}\), where \(ecn_k\) is a constant that may need to be adjusted to the specific chromatographic properties. The default value is \(ecn_k = 1.5\).

See also

Other QC plots: plot_feature_correlations(), plot_interference_correction(), plot_matrixeffects(), plot_normalization_qc(), plot_pca(), plot_pca_loading(), plot_qc_interference_impact(), plot_qc_summary_byclass(), plot_qc_summary_overall(), plot_qcmetrics_comparison(), plot_rla_boxplot(), plot_runscatter(), plot_runsequence()