QC Plots Sequencing metrics (Alignment) (Layout) — Seq_QC_Plot_Alignment

Plot a combined plot of the Alignment QC metrics from sequencing output.

Seq_QC_Plot_Alignment_Combined(
  metrics_dataframe,
  plot_by = "sample_id",
  colors_use = NULL,
  dot_size = 1,
  x_lab_rotate = FALSE,
  patchwork_title = "Sequencing QC Plots: Read Alignment Metrics",
  significance = FALSE,
  ...
)

Arguments

metrics_dataframe: data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).
plot_by: Grouping factor for the plot. Default is to plot as single group with single point per sample.
colors_use: colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
dot_size: size of the dots plotted if plot_by is not sample_id Default is 1.
x_lab_rotate: logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.
patchwork_title: Title to use for the patchworked plot output.
significance: logical. Whether to calculate and plot p-value comparisons when plotting by grouping factor. Default is FALSE.
...: Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

Value

A ggplot object

Examples

if (FALSE) {
Seq_QC_Plot_Alignment_Combined(metrics_dataframe = metrics)
}