polar_grid function

Grid required for 3D volcano plot and 2D radial plots

Generates a cylindrical grid of the appropriate dimensions for a 3D volcano plot

polar_grid(
  r_vector = NULL,
  z_vector = NULL,
  r_axis_ticks = NULL,
  z_axis_ticks = NULL,
  axis_angle = 5/6,
  n_spokes = 12,
  axes_from_origin = TRUE,
  ...
)

Arguments

• r_vector: An optional numerical vector for the radial coordinates. This is used to calculate breaks on the r axis using pretty. If this is NULL the r_axis_ticks are used as breaks.
• z_vector: An optional numerical vector for the z coordinates. This is used to calculate breaks on the z axis using pretty. If this is NULL the z_axis_ticks are used as breaks.
• r_axis_ticks: A numerical vector of breaks for the radial axis (used if r_vector is NULL).
• z_axis_ticks: A numerical vector of breaks for the z axis (used if z_vector is NULL).
• axis_angle: angle in radians to position the radial axis (default = 5/6)
• n_spokes: the number of outward spokes to be plotted (default = 12)
• axes_from_origin: Whether the axis should start at 0 or the first break (default = TRUE)
• ...: optional parameters for pretty on the r axis

Returns

Returns an S4 grid object containing:

• 'polar_grid' The coordinates for a radial grid
• 'axes' The axes features for 'plotly'
• 'axis_labels' The axis labels
• 'r' The grid radius
• 'z' The grid height
• 'text_coords' The coordinates for text labels
• 'n_r_breaks' The number of ticks on the r axis
• 'n_r_breaks' The number of ticks on the z axis

Examples

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

grid <- polar_grid(r_vector=syn_polar@df[[1]]$r,
           z_vector=NULL,
           r_axis_ticks = NULL,
           z_axis_ticks = c(0, 8, 16, 32),
           n_spokes = 4)

References

Lewis, Myles J., et al. (2019). c("\n", "Molecular portraits of early rheumatoid arthritis identify clinical and\n", "treatment response phenotypes.")

Cell reports, 28 :9