QC Plots Genes vs UMIs — QC_Plot_UMIvsGene • scCustomize

Custom FeatureScatter for initial QC checks including lines for thresholding

QC_Plot_UMIvsGene(
  seurat_object,
  x_axis_label = "UMIs per Cell/Nucleus",
  y_axis_label = "Genes per Cell/Nucleus",
  low_cutoff_gene = -Inf,
  high_cutoff_gene = Inf,
  low_cutoff_UMI = -Inf,
  high_cutoff_UMI = Inf,
  cutoff_line_width = NULL,
  colors_use = NULL,
  meta_gradient_name = NULL,
  meta_gradient_color = viridis_plasma_dark_high,
  meta_gradient_na_color = "lightgray",
  meta_gradient_low_cutoff = NULL,
  cells = NULL,
  combination = FALSE,
  ident_legend = TRUE,
  pt.size = 1,
  group.by = NULL,
  raster = NULL,
  raster.dpi = c(512, 512),
  ggplot_default_colors = FALSE,
  color_seed = 123,
  shuffle_seed = 1,
  ...
)

Arguments

seurat_object: Seurat object name.
x_axis_label: Label for x axis.
y_axis_label: Label for y axis.
low_cutoff_gene: Plot line a potential low threshold for filtering genes per cell.
high_cutoff_gene: Plot line a potential high threshold for filtering genes per cell.
low_cutoff_UMI: Plot line a potential low threshold for filtering UMIs per cell.
high_cutoff_UMI: Plot line a potential high threshold for filtering UMIs per cell.
cutoff_line_width: numerical value for thickness of cutoff lines, default is NULL.
colors_use: vector of colors to use for plotting by identity.
meta_gradient_name: Name of continuous meta data variable to color points in plot by. (MUST be continuous variable i.e. "percent_mito").
meta_gradient_color: The gradient color palette to use for plotting of meta variable (default is viridis "Plasma" palette with dark colors high).
meta_gradient_na_color: Color to use for plotting values when a meta_gradient_low_cutoff is set (default is "lightgray").
meta_gradient_low_cutoff: Value to use as threshold for plotting. meta_gradient_name values below this value will be plotted using meta_gradient_na_color.
cells: Cells to include on the scatter plot (default is all cells).
combination: logical (default FALSE). Whether or not to return a plot layout with both the plot colored by identity and the meta data gradient plot.
ident_legend: logical, whether to plot the legend containing identities (left plot) when combination = TRUE. Default is TRUE.
pt.size: Passes size of points to both FeatureScatter and geom_point.
group.by: Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Default is @active.ident.
raster: Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 cells.
raster.dpi: Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
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.
shuffle_seed: Sets the seed if randomly shuffling the order of points (Default is 1).
...: Extra parameters passed to FeatureScatter.

Value

A ggplot object

Examples

library(Seurat)
QC_Plot_UMIvsGene(seurat_object = pbmc_small, x_axis_label = "UMIs per Cell/Nucleus",
y_axis_label = "Genes per Cell/Nucleus")