volcano3D (version 2.0.9)

boxplot_trio: Boxplot to compare groups

Description

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

Usage

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",
  ...
)

Value

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

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

References

Lewis, Myles J., et al. (2019). Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell reports, 28:9

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")