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. The column name or number in polar@data to be analysed The fill colours for each box assigned in order of levels_order. Default = c('green3', 'blue', 'red') ). 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. A character vector stating the contrast groups to be plotted, in order. If NULL this defaults to the levels in polar@outcome. A list of contrasts to pass to stat_compare_means. If NULL (default) all contrast pvalues are calculated and plotted. The font size of text (default = 10) Colour to print statistics (default="black"). The font size of statistical parameter (default = 3). The distance between statistics on the y-axis (default = 0.05). Whether to use 'plotly' or 'ggplot'. Default is 'ggplot' Other parameters for stat_compare_means

## Value

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

## 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")