QC Plots Genes vs Misc

Custom FeatureScatter for initial QC checks including lines for thresholding

QC_Plot_GenevsFeature(
  seurat_object,
  feature1,
  x_axis_label = NULL,
  y_axis_label = "Genes per Cell/Nucleus",
  low_cutoff_gene = NULL,
  high_cutoff_gene = NULL,
  low_cutoff_feature = NULL,
  high_cutoff_feature = NULL,
  cutoff_line_width = NULL,
  colors_use = NULL,
  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.

feature1

First feature to plot.

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_feature

Plot line a potential low threshold for filtering feature1 per cell.

high_cutoff_feature

Plot line a potential high threshold for filtering feature1 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.

pt.size

Adjust point size for plotting.

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

if (FALSE) {
QC_Plot_GenevsFeature(seurat_object = obj, y_axis_label = "Feature per Cell")
}