volcano_trio: Volcano Plots for a three-way comparison

Description Usage Arguments Value References Examples

View source: R/volcano_trio.R

Description

This function creates a volcano plot for all combinations of groups in a factor.

Usage

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volcano_trio(
  polar,
  p_cutoff = 0.05,
  fc_cutoff = 1,
  label_rows = NULL,
  label_size = 3,
  text_size = 10,
  marker_size = 0.7,
  shared_legend_size = 1,
  sig_names = NULL,
  colours = c("grey60", "salmon", "steelblue", "limegreen"),
  fc_line = TRUE,
  p_line = TRUE,
  line_colours = c("black", "black"),
  share_axes = TRUE
)

Arguments

polar

A polar object with the pvalues between groups of interest. Created by polar_coords.

p_cutoff

The cut-off for pvalue significance (default = 0.05).

fc_cutoff

The cut-off for fold change significance (default = 1).

label_rows

Row numbers or names of values to be annotated/labelled (default = NULL).

label_size

The font size of labels (default = 3)

text_size

The font size of text (default = 10)

marker_size

The size of markers (default = 0.7)

shared_legend_size

The size for the legend (default = 1).

sig_names

A character vector of labels to be used for: non-significant; adjusted p < p_cutoff; |Fold Change| > fc_cutoff; and finally adjusted p < p_cutoff. If NULL c('Not Significant', paste('Padj <', `p_cutoff`), paste('|FC| >', `fc_cutoff`), paste('Padj <', `p_cutoff`, 'and |FC| >', `fc_cutoff`)) is used.

colours

A character vector of colours to be used for non-significant; adjusted p < p_cutoff; |Fold Change| >, fc_cutoff; and adjusted p < p_cutoff. default = p_cutoff & |Fold Change| > fc_cutoff markers respectively (default = c('grey60', 'salmon', 'steelblue', 'limegreen')).

fc_line

Logical whether to add vertical dashed line at fc_cutoff (default = TRUE).

p_line

Logical whether to add horizontal dashed line at p_cutoff (default = TRUE).

line_colours

A character vector stating the colour of lines to be used for fc_line and p_line respectively (default = c('black', 'black')).

share_axes

Logical whether plots should share axes when plotted together.

Value

Returns a list of ggplot volcano plots. The first three elements contain comparisons between all contrasts. The last element in the list is a combined figure for all three plots.

References

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

Examples

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data(example_data)
syn_polar <- polar_coords(sampledata = syn_example_meta,
                          contrast = "Pathotype",
                          groups = NULL,
                          pvalues = syn_example_p,
                          expression = syn_example_rld,
                          p_col_suffix = "pvalue",
                          padj_col_suffix = "padj",
                          non_sig_name = "Not Significant",
                          multi_group_prefix = "LRT",
                          significance_cutoff = 0.01,
                          fc_col_suffix='log2FoldChange',
                          fc_cutoff = 0.3)
syn_volcano_plots <- volcano_trio(polar=syn_polar)
syn_volcano_plots$All

volcano3D documentation built on July 1, 2020, 9:56 p.m.