radial_plotly: Three-way radial comparison Polar Plot (using plotly)
In volcano3D: Interactive Plotting of Three-Way Differential Expression Analysis

Description Usage Arguments Value References Examples

This function creates an interactive plotly object which maps differential expression onto a polar coordinates.

radial_plotly(
  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 = 50,
  grid = NULL,
  fc_or_zscore = "zscore",
  label_size = 14,
  colour_code_labels = TRUE,
  label_colour = NULL,
  grid_colour = "grey80",
  axis_colour = "black",
  marker_size = 6,
  marker_alpha = 0.7,
  marker_outline_colour = "white",
  marker_outline_width = 0.5,
  axis_title_size = 16,
  axis_label_size = 10,
  axis_ticks = NULL,
  axis_angle = 5/6,
  plot_height = 700,
  plot_width = 700,
  ...
)

`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 6) to offset the continuous colour scale by. This is calculated by converting the angle to a hue using `hsv` where 0 corresponds to the colour scale starting with red and 360 with magenta (default = 2).
`label_rows`	A vector of row names or numbers to label.
`arrow_length`	The length of label arrows (default = 50).
`grid`	An optional grid object. If NULL this will be calculated using the 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 = 14)
`colour_code_labels`	Logical whether label annotations should be colour coded. If FALSE label_colour is used.
`label_colour`	HTML 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").
`marker_size`	Size of the markers (default = 6).
`marker_alpha`	Opacity for the markers (default = 0.7).
`marker_outline_colour`	Colour for marker outline (default = white)
`marker_outline_width`	Width for marker outline (default = 0.5)
`axis_title_size`	Font size for axis titles (default = 16)
`axis_label_size`	Font size for axis labels (default = 10)
`axis_ticks`	A numerical vector of radial axis tick breaks. If NULL this will be calculated using `pretty`.
`axis_angle`	Angle in radians for the radial axis (default = 5/6).
`plot_height`	Plot height in px (default=700).
`plot_width`	Plot width in px (default=700).
`...`	Optional parameters to pass to `polar_grid`.

Returns a plotly plot featuring variables on a tri-axis radial graph

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

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_plotly(polar = syn_polar, label_rows = c("SLAMF6"))