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fSuSiE Plots

Source: R/plot_functions.R
fsusie_plots.Rd

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.