plot.feature_calculations {theftdlc}

Produce a plot for a feature_calculations object

Description

Produce a plot for a feature_calculations object

Usage

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

Arguments

x

feature_calculations object containing the raw feature matrix produced by theft::calculate_features

type

character specifying the type of plot to draw. Defaults to "quality"

norm_method

character specifying a rescaling/normalising method to apply if type = "matrix" or if type = "cor". Can be one of "z-score", "Sigmoid", "RobustSigmoid", or "MinMax". Defaults to "z-score"

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"

Value

object of class ggplot that contains the graphic

Author(s)

Trent Henderson