Plot deviations — plot_deviation • iCOBRA

Plot the deviations between observed scores and the continuous truth variable.

Usage

plot_deviation(
  cobraplot,
  title = "",
  stripsize = 15,
  titlecol = "black",
  xaxisrange = NULL,
  plottype = "boxplot",
  dojitter = TRUE,
  transf = "raw"
)

Arguments

cobraplot: A COBRAPlot object.
title: A character string giving the title of the plot.
stripsize: A numeric value giving the size of the strip text, when the results are stratified by an annotation.
titlecol: A character string giving the color of the title.
xaxisrange: A numeric vector with two elements, giving the lower and upper boundary of the x-axis, respectively.
plottype: Either "boxplot" or "violinplot", indicating what type of plot to make.
dojitter: A logical indicating whether to include jittered data points or not.
transf: A character indicating the transformation to apply to the deviations before plotting. Must be one of "raw", "absolute" or "squared"

Value

A ggplot object

Author

Charlotte Soneson

Examples

data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example, cont_truth = "logFC",
                                   aspects = "deviation")
#> Warning: Object doesn't have a slot sval. Please run update_cobradata(). For consistency, I will return an empty data.frame
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
                                   incltruth = TRUE)
plot_deviation(cobraplot)
#> Warning: Removed 4377 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 4377 rows containing missing values or values outside the scale range
#> (`geom_point()`).