volcano3D (version 1.2.0)

radial_ggplot: 'Ggplot' for Three Way Polar Plot

Description

This function creates a radar plot using 'ggplot' for a three-way comparison

Usage

radial_ggplot(
  polar,
  colours = c("green3", "cyan", "blue", "purple", "red", "gold2"),
  non_sig_colour = "grey60",
  colour_scale = "discrete",
  continuous_shift = 1.33,
  label_rows = NULL,
  arrow_length = 1,
  grid = NULL,
  fc_or_zscore = "zscore",
  label_size = 5,
  colour_code_labels = TRUE,
  label_colour = NULL,
  grid_colour = "grey80",
  axis_colour = "black",
  axis_title_size = 5,
  axis_label_size = 3,
  marker_alpha = 0.7,
  marker_size = 3,
  marker_outline_colour = "white",
  marker_outline_width = 0.5,
  axis_angle = 1/6,
  legend_size = 20,
  ...
)

Arguments

polar

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

colours

A vector of colour names or hex triplets for each of the six groups. Default = c("green3", "cyan", "blue", "purple", "red", "gold2"). Colours are assigned in order: group1+, group1+group2+, group2+, group2+group3+, group3+, group1+group3+.

non_sig_colour

The colour for non-significant markers (default = "grey60").

colour_scale

whether to use a "discrete" or "continuous" colour scale (default = "discrete").

continuous_shift

the number of radians (between 0 and 2) corresponding to the angle to offset the continuous colour scale by. The continuous colour scale is calculated by converting the angle to hue where 0 corresponds to red and 2 to magenta (default = 1.33).

label_rows

A vector of row names or numbers to label.

arrow_length

length of label arrow (default = 1).

grid

An optional grid object. If NULL this will be calculated using default values of polar_grid.

fc_or_zscore

Whether to use the z-score or fold change as magnitude. Options are 'zscore' (default) or 'fc'.

label_size

Font size of labels/annotations (default = 5).

colour_code_labels

Logical whether label annotations should be colour coded. If FALSE label_colour is used.

label_colour

Colour of annotation labels if not colour coded.

grid_colour

The colour of the grid (default="grey80").

axis_colour

The colour of the grid axes and labels (default="black").

axis_title_size

Font size for axis titles (default = 5)

axis_label_size

Font size for axis labels (default = 3)

marker_alpha

The alpha parameter for markers (default = 0.7).

marker_size

Size of the markers (default = 3).

marker_outline_colour

Colour for marker outline (default = white)

marker_outline_width

Width for marker outline (default = 0.5)

axis_angle

Angle for the radial axis labels in pi radians (default = 1/6).

legend_size

Size for the legend text (default = 20).

...

Optional grid parameters to pass to polar_grid.

Value

Returns a polar 'ggplot' object featuring variables on a tri-axis radial graph

References

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

Examples

# NOT RUN {
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_cutoff = 0.3)

radial_ggplot(polar = syn_polar, label_rows = c("SLAMF6"))
# }