plot.syndromics: Method to plot results from pc_stability or permut_pca_test

In ucsf-ferguson-lab/syndRomics: Component loading interpretation and visualization with syndromic plots

Method to plot results from pc_stability or permut_pca_test

Description

S3 method of object class "syndromics" returned by pc_stability() or permut_pca_test() for the generic plot() function. This function is a wrapper to the plotting functions in the syndromics package to make plotting faster from the object class "syndromics" returned by pc_stability() or permut_pca_test() for the generic plot() function.

see each plotting function for details in other arguments.

Usage

## S3 method for class 'syndromics'
plot(
  x,
  plot_type = "barmap",
  ndim = NULL,
  plot_resample = F,
  communalities = F,
  ...
)

Arguments

x	Object class "syndromics" returned by pc_stability() or permut_pca_test()
plot_type	character string specifying the type of the plot. The function will automatically select a type of plot that is most adequate, but it can be changed. The options are barmap, heatmap, syndromics and VAF.
ndim	Numeric. Number of dimensions to plot.
plot_resample	Logical. Whether to plot the resamples from pc_stability() or permut_pca_test() in barmap plots. If set to TRUE, confidence intervals will be plotted.
communalities	Logical. Whether communalities using barmap should be plotted rather than loadings.
...	Further arguments pass down to the corresponding plotting function.

Author(s)

Abel Torres Espin

ucsf-ferguson-lab/syndRomics documentation built on June 26, 2022, 5:36 p.m.