scmet_plot_mean_var | R Documentation |
Function for plotting mean methylation on x-axis and variability on y-axis (either overdispersion or residual overdispersion). If HVF/LVF analysis is performed, points will be also coloured accordingly.
scmet_plot_mean_var( obj, y = "gamma", task = NULL, show_fit = TRUE, title = NULL, nfeatures = NULL, n = 80 )
obj |
The scMET object after calling the |
y |
The parameter to plot on the y-axis. Values can be |
task |
If NULL (default) the mean-variability relationship is plotted. If set to "hvf" or "lvf", points are coloured according the HVF/LVF analysis task. |
show_fit |
Logical, whether to show the fitted mean-overdispersion
trend. Applicable only when |
title |
Optional title, default NULL. |
nfeatures |
Optional parameter, denoting a subset of number of features
to plot. Mostly to reduce over-plotting. When |
n |
Optional integer denoting the number of grid points to colour them
by density. Used by |
A ggplot2 object.
C.A.Kapourani C.A.Kapourani@ed.ac.uk
scmet
, scmet_differential
,
scmet_hvf_lvf
, scmet_plot_vf_tail_prob
,
scmet_plot_efdr_efnr_grid
, scmet_plot_volcano
,
scmet_plot_ma
# Fit scMET obj <- scmet(Y = scmet_dt$Y, X = scmet_dt$X, L = 4, iter = 100) scmet_plot_mean_var(obj = obj, y = "gamma")
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