cpam (version 0.1.3)

plot_cpam: Plot fitted changepoint additive models

Description

Plot fitted changepoint additive models

Usage

plot_cpam(
  cpo,
  gene_id = NULL,
  target_id = NULL,
  cp_type = c("cp_1se", "cp_min"),
  shape_type = "shape1",
  bs = "auto",
  cp_fix = -1,
  facet = FALSE,
  sp = NULL,
  show_fit = TRUE,
  show_data = TRUE,
  show_fit_ci = TRUE,
  show_data_ci = TRUE,
  ci_prob = "se",
  remove_null = FALSE,
  null_threshold = 0.05,
  null_threshold_adj = TRUE,
  k_mult = 1.2,
  return_fits_only = FALSE,
  family = "nb",
  common_y_scale = TRUE,
  scaled = FALSE,
  base_size = 12
)

Value

a ggplot object

Arguments

cpo

A cpam object containing count data, model fits, and optional changepoint/shape estimates

gene_id

character; gene_id (mutually exclusive with target_id)

target_id

character; target_id (mutually exclusive with gene_id)

cp_type

One of "cp_1se" or "cp_min"; rule for selecting changepoint from fitted models. See estimate_changepoint() for details.

shape_type

One of "shape1" or "shape2"; which set of fitted shape patterns to use. See select_shape() for details.

bs

Shape pattern to fit ("null", "lin", "ilin", "dlin", or from cpo$bss). Use "auto" (default) to use estimated shapes as per shape_type.

cp_fix

Numeric; fixed changepoint time. Set to -1 (default) to use estimated changepoints

facet

Logical; for multiple transcripts, plot in separate facets?

sp

numerical; set the smooth parameter. NULL (default) for automatic selection

show_fit

logical; show the fitted trend?

show_data

logical; show (possibly normalized and scaled) data points?

show_fit_ci

logical; show credible interval for the fitted trend?

show_data_ci

logical; show bootstrapped quantile for data points?

ci_prob

"se" for standard error bands (see mgcv::predict.gam()), or numeric for simulation-based intervals. If numerical, sets the probability for the simulation-based estimates of credible interval.

remove_null

logical; only plot differentially expressed transcripts (not applicable for gene-only analyses)

null_threshold

numeric; P value threshold for filtering out NULL transcripts

null_threshold_adj

logical; use adjusted (default) or non-adjusted p-values for filtering targets

k_mult

numerical; multiplier for the number of knots in the spline. Not recommended to change this value.

return_fits_only

logical; return the model fits. Does not plot the function

family

character; negative binomial ("nb", default) or Gaussian ("gaussian")

common_y_scale

logical; for faceted plots of multiple transcripts, should the scale of the y-axis be common or free.

scaled

logical; scaled data by overdispersions (for bootstrapped data only)

base_size

numeric; base font size for the plot

Details

Plots the fitted trend and data points for a given gene or target. If a gene ID is supplied, the function will plot all transcripts for that gene. The function can also be used to return the model fit(s) only, which are gamObject objects from the mgcv package.

Examples

library(cpam)

# load gene-only example cpam object
load(system.file("extdata", "cpo_example.rda", package = "cpam"))

# example gene
plot_cpam(cpo_example, gene_id = "g003")

# gene with estimated changepoint at timepoint 3
plot_cpam(cpo_example, gene_id = "g013")

# manually set the changepoint
plot_cpam(cpo_example, gene_id = "g013", cp_fix = 2)