Plot observed UMI counts and model
Plot observed UMI counts and model
plot_model( x, umi, goi, x_var = x$arguments$latent_var[1], cell_attr = x$cell_attr, do_log = TRUE, show_fit = TRUE, show_nr = FALSE, plot_residual = FALSE, batches = NULL, as_poisson = FALSE, arrange_vertical = TRUE, show_density = FALSE, gg_cmds = NULL )
x |
The output of a vst run |
umi |
UMI count matrix |
goi |
Vector of genes to plot |
x_var |
Cell attribute to use on x axis; will be taken from x$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 |
A ggplot object
vst_out <- vst(pbmc, return_cell_attr = TRUE) plot_model(vst_out, pbmc, 'EMC4')
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.