QC Plots Cell "Complexity"

Source: R/QC_Plotting_Seurat.R

Custom VlnPlot for initial QC checks including lines for thresholding

QC_Plots_Complexity(
  seurat_object,
  feature = "log10GenesPerUMI",
  group.by = NULL,
  x_axis_label = NULL,
  y_axis_label = "log10(Genes) / log10(UMIs)",
  plot_title = "Cell Complexity",
  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.

feature

Feature from Meta Data to plot.

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.

plot_title

Plot Title.

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)
pbmc_small <- Add_Cell_Complexity(pbmc_small)

QC_Plots_Complexity(seurat_object = pbmc_small)