Step: Plot QC

Generate quality control plots for the experiment using glyclean plotting functions. This step can be used before AND after step_preprocess() to generate QC plots at different stages.

Usage

step_plot_qc(
  when = "post",
  batch_col = "batch",
  rep_col = NULL,
  plot_width = 7,
  plot_height = 5
)

Arguments

when: Character string indicating when this QC step is run. Use "pre" for pre-preprocessing QC, "post" for post-preprocessing QC, or any other value for generic QC. This is appended to the step ID. Default is "post".
batch_col: Column name for batch information (for glyclean::plot_batch_pca()).
rep_col: Column name for replicate information (for glyclean::plot_rep_scatter()).
plot_width: Width of plots in inches. Default is 7.
plot_height: Height of plots in inches. Default is 5.

Value

A glysmith_step object.

Details

Data required:

exp: The experiment to plot QC for

Plots generated:

qc_missing_heatmap: Missing value heatmap
qc_missing_samples_bar: Missing value bar plot on samples
qc_missing_variables_bar: Missing value bar plot on variables
qc_tic_bar: Total intensity count bar plot
qc_rank_abundance: Rank abundance plot
qc_int_boxplot: Intensity boxplot
qc_rle: RLE plot
qc_cv_dent: CV density plot
qc_batch_pca: PCA score plot colored by batch (if batch_col provided)
qc_rep_scatter: Replicate scatter plots (if rep_col provided)

When when = "pre", plots are prefixed with qc_pre_ to distinguish from post-QC plots. When when = "post" or NULL, plots use the standard qc_ prefix.

AI Prompt

This section is for AI in inquire_blueprint() only.

By default, include this step ONLY after step_preprocess().
You MUST provide the when parameter to specify when the QC is being run.

Examples

step_plot_qc(when = "pre")
#> <step "step_plot_qc(when = \"pre\")"> QC (pre-preprocessing)
step_plot_qc(when = "post")
#> <step "step_plot_qc(when = \"post\")"> QC (post-preprocessing)