radial_ggplot {volcano3D}

'Ggplot' for Three Way Polar Plot

Description

This function creates a 3-way polar plot using 'ggplot' for a three-class comparison.

Usage

radial_ggplot(
  polar,
  type = 1,
  colours = NULL,
  label_rows = NULL,
  arrow_length = 1,
  label_size = 5,
  colour_code_labels = FALSE,
  label_colour = "black",
  grid_colour = "grey80",
  grid_width = 0.7,
  axis_colour = "black",
  axis_width = 1,
  axis_title_size = 5,
  axis_label_size = 3,
  marker_alpha = 0.7,
  marker_size = 3,
  marker_outline_colour = "white",
  marker_outline_width = 0.5,
  legend_size = 20,
  ...
)

Arguments

polar

A 'volc3d' object with the p-values between groups of interest and polar coordinates created by polar_coords, deseq_polar or voom_polar.

type

Numeric value whether to use scaled (z-score) or unscaled (fold change) as magnitude. Options are 1 = z-score (default) or 2 = unscaled/fold change.

colours

A vector of colours for the non-significant points and each of the six groups.

label_rows

A vector of row names or indices to label

arrow_length

The length of label arrows

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")

grid_width

The width of the axis lines (default=0.6)

axis_colour

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

axis_width

The width of the axis lines (default=1)

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)

legend_size

Size for the legend text (default = 20).

...

Optional parameters passed to polar_grid e.g. r_axis_ticks or axis_angle

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

See Also

polar_coords

Examples

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

radial_ggplot(polar = syn_polar, label_rows = c("COBL"))