QC Plots Genes — QC_Plots_Genes • scCustomize

Custom VlnPlot for initial QC checks including lines for thresholding

QC_Plots_Genes(
  seurat_object,
  plot_title = "Genes Per Cell/Nucleus",
  group.by = NULL,
  x_axis_label = NULL,
  y_axis_label = "Features",
  low_cutoff = NULL,
  high_cutoff = NULL,
  pt.size = NULL,
  plot_median = FALSE,
  plot_boxplot = FALSE,
  median_size = 15,
  colors_use = NULL,
  x_lab_rotate = TRUE,
  y_axis_log = FALSE,
  raster = NULL,
  ggplot_default_colors = FALSE,
  color_seed = 123,
  ...
)

Arguments

seurat_object: Seurat object name.
plot_title: Plot Title.
group.by: Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.
x_axis_label: Label for x axis.
y_axis_label: Label for y axis.
low_cutoff: Plot line a potential low threshold for filtering.
high_cutoff: Plot line a potential high threshold for filtering.
pt.size: Point size for plotting.
plot_median: logical, whether to plot median for each ident on the plot (Default is FALSE).
plot_boxplot: logical, whether to plot boxplot inside of violin (Default is FALSE).
median_size: Shape size for the median is plotted.
colors_use: vector of colors to use for plot.
x_lab_rotate: Rotate x-axis labels 45 degrees (Default is TRUE).
y_axis_log: logical. Whether to change y axis to log10 scale (Default is FALSE).
raster: Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).
ggplot_default_colors: logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
color_seed: random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.
...: Extra parameters passed to VlnPlot.

Value

A ggplot object

Examples

library(Seurat)
QC_Plots_Genes(seurat_object = pbmc_small, plot_title = "Genes per Cell", low_cutoff = 40,
high_cutoff = 85)