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RunSequence plot

Source: R/plots-qc-runorder.R
plot_runsequence.Rd

The RunSequence plot provides an overview of the analysis design and timelines, which can be useful for subsequent processing steps. The plot illustrates the batch structure, the quality control (QC) samples included with their respective positions, and additional information regarding the date, duration, and run time of the analysis.

Setting show_timestamp = TRUE allows you to check for any interruptions in the analysis timeline.

Usage

plot_runsequence(
  data = NULL,
  qc_types = NA,
  show_batches = TRUE,
  show_timestamp = FALSE,
  add_info_title = TRUE,
  single_row = FALSE,
  segment_linewidth = 0.5,
  batch_zebra_stripe = FALSE,
  batch_line_color = "#b6f0c5",
  batch_fill_color = "grey93",
  font_base_size = NULL,
  legend_position = NULL,
  legend_size = NULL,
  show_legend_title = NULL,
  title = NULL
)

Arguments

data

A MRMhubExperiment object.

qc_types

QC types to be plotted. Can be a vector of QC types or a regular expression pattern. NA (default) displays all available QC/Sample types.

show_batches

Logical, whether to show batch separators in the plot.

show_timestamp

Logical, whether to use the acquisition timestamp as the x-axis instead of the run sequence number.

add_info_title

Logical, whether to add a title with the experiment title, analysis date, and analysis times.

single_row

Logical, whether to show all QC types in a single row.

segment_linewidth

Width of the segment lines, default is 0.5.

batch_zebra_stripe

Logical, whether to show batches as shaded areas instead of line separators.

batch_line_color

Color of the batch separator lines.

batch_fill_color

Color of the batch shaded areas.

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).

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.

Value

A ggplot object representing the run sequence plot.

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_rt_vs_chain(), plot_runscatter()