plot_pseudotime_model: Plot the fit in pseudotime

Description Usage Arguments Value Examples

View source: R/embeddr.R

Description

Plot the fit in pseudotime

Usage

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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 [email protected] will be set to [email protected]

line_color

The colour of the predicted expression line to draw

...

Additional arguments to fit_pseudotime_models

Value

An plot object from ggplot

Examples

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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 18, 2017, 7:45 p.m.