QC_Plot_GenevsFeature {scCustomize} | R Documentation |
QC Plots Genes vs Misc
Description
Custom FeatureScatter for initial QC checks including lines for thresholding
Usage
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,
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. |
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 |
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 |
color_seed |
random seed for the "varibow" palette shuffle if |
shuffle_seed |
Sets the seed if randomly shuffling the order of points (Default is 1). |
... |
Extra parameters passed to |
Value
A ggplot object
Examples
## Not run:
QC_Plot_GenevsFeature(seurat_object = obj, y_axis_label = "Feature per Cell")
## End(Not run)