Seq_QC_Plot_Alignment_Combined: QC Plots Sequencing metrics (Alignment) (Layout)

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

QC Plots Sequencing metrics (Alignment) (Layout)

Description

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

Usage

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

## Not run: 
Seq_QC_Plot_Alignment_Combined(metrics_dataframe = metrics)

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.