boxplot_trio function

Boxplot to compare groups

Plots the expression of a specific row in expression to compare the three groups in a boxplot using either ggplot or plotly.

boxplot_trio(
  polar,
  value,
  box_colours = c("green3", "blue", "red"),
  test = "polar_pvalue",
  levels_order = NULL,
  my_comparisons = NULL,
  text_size = 10,
  stat_colour = "black",
  stat_size = 3,
  step_increase = 0.05,
  plot_method = "ggplot",
  ...
)

Arguments

• polar: A 'volc3d' object including expression data from groups of interest. Created by polar_coords.

• value: The column name or number in polar@data to be analysed

• box_colours: The fill colours for each box assigned in order of levels_order. Default = c('green3', 'blue', 'red') ).

• test: The statistical test used to compare expression. Allowed values include:

  • polar_pvalue (default) and 'polar_padj' for the pvalues and adjusted pvalues in the polar object.
  • polar_multi_pvalue and polar_multi_padj for the pvalues and adjusted pvalues across all groups using the polar@multi_group_test columns.
  • t.test (parametric) and wilcox.test (non-parametric). Perform comparison between groups of samples.
  • anova (parametric) and kruskal.test (non-parametric). Perform one-way ANOVA test comparing multiple groups.

• levels_order: A character vector stating the contrast groups to be plotted, in order. If NULL this defaults to the levels in polar@outcome.

• my_comparisons: A list of contrasts to pass to stat_compare_means. If NULL (default) all contrast pvalues are calculated and plotted.

• text_size: The font size of text (default = 10)

• stat_colour: Colour to print statistics (default="black").

• stat_size: The font size of statistical parameter (default = 3).

• step_increase: The distance between statistics on the y-axis (default = 0.05).

• plot_method: Whether to use 'plotly' or 'ggplot'. Default is 'ggplot'

• ...: Other parameters for stat_compare_means

Returns

Returns a boxplot featuring the differential expression between groups in comparison with annotated pvalues.

Examples

data(example_data)
syn_polar <- polar_coords(outcome = syn_example_meta$Pathotype,
                          data = t(syn_example_rld))

boxplot_trio(syn_polar, value = "COBL", plot_method="plotly")
boxplot_trio(syn_polar, value = "COBL")

References

Lewis, Myles J., et al. (2019). c("\n", "Molecular portraits of early rheumatoid arthritis identify clinical and\n", "treatment response phenotypes.")

Cell reports, 28 :9