plot.feature_calculations: Produce a plot for a feature_calculations object

Description

Produce a plot for a feature_calculations object

Usage

# S3 method for feature_calculations
plot(
  x,
  type = c("matrix", "cor", "violin", "box", "quality"),
  norm_method = c("zScore", "Sigmoid", "RobustSigmoid", "MinMax", "MaxAbs"),
  unit_int = FALSE,
  clust_method = c("average", "ward.D", "ward.D2", "single", "complete", "mcquitty",
    "median", "centroid"),
  cor_method = c("pearson", "spearman"),
  feature_names = NULL,
  ...
)

Value

object of class ggplot that contains the graphic

Arguments

x: feature_calculations object containing the raw feature matrix produced by theft::calculate_features
type: character specifying the type of plot to draw. Can be one of "matrix", "cor", "violin", "box", or "quality". Defaults to "matrix"
norm_method: character specifying a rescaling/normalising method to apply if type = "matrix" or if type = "cor". Can be one of "zScore", "Sigmoid", "RobustSigmoid", "MinMax", or "MaxAbs". Defaults to "zScore"
unit_int: Boolean whether to rescale into unit interval [0,1] after applying normalisation method. Defaults to FALSE
clust_method: character specifying the hierarchical clustering method to use if type = "matrix" or if type = "cor". Defaults to "average"
cor_method: character specifying the correlation method to use if type = "cor". Defaults to "pearson"
feature_names: character vector denoting the name of the features to plot if type = "violin". Defaults to NULL
...: Arguments to be passed to ggplot2::geom_bar if type = "quality", ggplot2::geom_raster if type = "matrix", ggplot2::geom_raster if type = "cor", or ggplot2::geom_point if type = "violin"

Author

Trent Henderson