plot_model: Plot observed UMI counts and model

In sctransform: Variance Stabilizing Transformations for Single Cell UMI Data

Plot observed UMI counts and model

Description

Plot observed UMI counts and model

Usage

plot_model(
  x,
  umi,
  goi,
  x_var = x$arguments$latent_var[1],
  cell_attr = x$cell_attr,
  do_log = TRUE,
  show_fit = TRUE,
  show_nr = FALSE,
  plot_residual = FALSE,
  batches = NULL,
  as_poisson = FALSE,
  arrange_vertical = TRUE,
  show_density = FALSE,
  gg_cmds = NULL
)

Arguments

x	The output of a vst run
umi	UMI count matrix
goi	Vector of genes to plot
x_var	Cell attribute to use on x axis; will be taken from x$arguments$latent_var[1] by default
cell_attr	Cell attributes data frame; will be taken from x$cell_attr by default
do_log	Log10 transform the UMI counts in plot
show_fit	Show the model fit
show_nr	Show the non-regularized model (if available)
plot_residual	Add panels for the Pearson residuals
batches	Manually specify a batch variable to break up the model plot in segments
as_poisson	Fix model parameter theta to Inf, effectively showing a Poisson model
arrange_vertical	Stack individual ggplot objects or place side by side
show_density	Draw 2D density lines over points
gg_cmds	Additional ggplot layer commands

Value

A ggplot object

Examples

vst_out <- vst(pbmc, return_cell_attr = TRUE)
plot_model(vst_out, pbmc, 'EMC4')

sctransform documentation built on Oct. 19, 2023, 9:08 a.m.