plot_pseudotime_model: Plot the fit in pseudotime

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

Plot the fit in pseudotime

Usage

plot_pseudotime_model(sce, models = NULL, n_cores = 2,
  facet_wrap_scale = "fixed", use_log_scale = FALSE, color_by = NULL,
  nrow = NULL, ncol = NULL, mask_min_expr = TRUE, line_color = "red",
  ...)

Arguments

sce	An object of class SCE set
models	A list of models returned by fit_pseudotime_models. If NULL (default), these will be re-calculated
n_cores	Number of cores to use when calculating the pseudotime models if 'model' is NULL
facet_wrap_scale	Passed to the scales argument in facet_wrap. Should scales be fixed ('fixed', the default), free ('free'), or free in one dimension ('free_x', 'free_y')
use_log_scale	Logical If TRUE scale_y_log10 is added to plot
color_by	The variable in pData(sce) by which to colour the points
nrow	Number of rows to be passed to ggplot2::facet_wrap
ncol	NUmber of columns to be passed to ggplot2::facet_wrap
mask_min_expr	Logical. If TRUE (default) any predicted expression less than sce@lowerDetectionLimit will be set to sce@lowerDetectionLimit
line_color	The colour of the predicted expression line to draw
...	Additional arguments to fit_pseudotime_models

Value

An plot object from ggplot

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- fit_pseudotime(sce)
plot_pseudotime_model(sce[1,]) # select first gene

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.