plot_expr_by_numeric_var: Plot Gene Expression for Samples against Numerical Variable

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Plot Gene Expression for Samples against Numerical Variable

Description

Equivalent of plot_violin with a numeric x-axis.

Usage

plot_expr_by_numeric_var(
  sce,
  numeric_var = "p_tau",
  subset_var = "cluster_celltype",
  subset_group = "Oligo",
  gene = "PLP1",
  alpha = 0.05,
  size = 0.01,
  label_angle = 0
)

Arguments

sce	a SingleCellExperiment object
numeric_var	The colData variable for x-axis groups. Default is p_tau
subset_var	The colData variable to subset on
subset_group	The specific subset_var group to subset
gene	The gene of interest
alpha	point alpha
size	point size
label_angle	The angle of x-axis labels (e.g. 0, 45)

Details

Generates a scatter plot of log2(counts+1) expression against numeric var. An additional plot of proportion of cells with non-zero counts per sample. Fits a linear model with confidence intervals for each plot.

Value

p a ggplot object

See Also

Other plotting functions: plot_reduced_dim(), plot_reduced_dim_gene(), plot_violin()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.