fsusie_plots: fSuSiE Plots

In stephenslab/susiF.alpha: Sum of Single Functions

fSuSiE Plots

Description

Various visualizations of fSuSiE results.

Usage

plot_susiF(
  obj,
  which_plot = c("both", "pip", "effect"),
  effect = "all",
  cred_band = TRUE,
  show_affected_region = TRUE,
  show_outing_grid = ifelse(diff(range(diff(obj$outing_grid))) < 1e-06, FALSE, TRUE),
  lfsr_curve = TRUE,
  line_width = 0.35,
  point_size = 1.25,
  dot_size = 0.5,
  pos_SNP,
  point_shape,
  font_size = 10,
  title = "",
  ...
)

## S3 method for class 'susiF'
plot(x, ...)

plot_susiF_pip(
  obj,
  title = "",
  pos_SNP,
  point_shape,
  point_size = 1.25,
  font_size = 10
)

plot_susiF_effect(
  obj,
  effect = "all",
  title = "",
  cred_band = TRUE,
  show_affected_region = TRUE,
  show_outing_grid = ifelse(diff(range(diff(obj$outing_grid))) < 1e-06, FALSE, TRUE),
  lfsr_curve = TRUE,
  line_width = 0.35,
  dot_size = 0.5,
  font_size = 10
)

Arguments

obj	Output of the susiF function.
which_plot	Which plots to return; a PIP plot, effect plot, or both (in which case the return value is a list containing the two plots.
effect	The indices of the effects to be plotted, or use effect = "all" to plot all effects.
cred_band	logical. If TRUE, plot credible bands if the fSuSiE model was fitted with wavelet regression.
show_affected_region	If show_affected_region = TRUE, the regions in which the credible bands cross zero are also shown.
show_outing_grid	If show_outing_grid = TRUE, show the grid positions at which the effects were estimated. By default, this option is set to TRUE only when the grid poisitions are uneven.
lfsr_curve	Logical. If TRUE, plot estimated lfsr of the effect at each base pair if obj fitted with HMM regression. This has no effect unless the susiF option post_processing = "HMM" was used.
line_width	Numeric. Width of the plotted lines.
point_size	numeric, size of the points.
dot_size	numeric, size of the points in the effect plot.
pos_SNP	vector, containing the base pair of the SNPs
point_shape	vector, containing the shape of dots
font_size	Passed as the “ont_size” argument to theme_cowplot.
title	The title of the plot.
...	additional arguments
x	Output of the susiF function.

stephenslab/susiF.alpha documentation built on March 1, 2025, 4:28 p.m.