volcano3D: Three-Dimensional Volcano Plot
In volcano3D: Interactive Plotting of Three-Way Differential Expression Analysis

Description Usage Arguments Value References Examples

Plots the pvalues from three-way comparisons in 3D space using plotly.

volcano3D(
  polar,
  colours = c("green3", "cyan", "blue", "purple", "red", "gold2"),
  non_sig_colour = "grey60",
  colour_scale = "discrete",
  continuous_shift = 1.33,
  label_rows = c(),
  grid = NULL,
  fc_or_zscore = "zscore",
  label_size = 14,
  arrow_length = 50,
  colour_code_labels = TRUE,
  label_colour = NULL,
  grid_colour = "grey80",
  axis_colour = "black",
  marker_size = 2.7,
  marker_alpha = 1,
  marker_outline_colour = "white",
  marker_outline_width = 0,
  axis_angle = 0.5,
  z_aspectratio = 1,
  xy_aspectratio = 1,
  plot_height = 700,
  ...
)

`polar`	A polar object with 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 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 2 with magenta (default = 2).
`label_rows`	A vector of row names or numbers to label.
`grid`	An optional grid object. If NULL this will be calculated using default values of `polar_grid`.
`fc_or_zscore`	whether to use fold change or z-score for the p-values. Options are 'zscore' (default) or 'fc').
`label_size`	font size for labels (default = 14).
`arrow_length`	The length of label arrows (default = 50).
`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 cylindrical grid (default="grey80").
`axis_colour`	The colour of the grid axes and labels (default="black").
`marker_size`	Size of the markers (default = 2.7).
`marker_alpha`	Opacity for the markers (default = 1).
`marker_outline_colour`	Colour for marker outline (default = white)
`marker_outline_width`	Width for marker outline (default = 0)
`axis_angle`	Angle in radians for the z axis (default = 0.5).
`z_aspectratio`	The aspect ratio for the z axis compared to x and y (default = 1). Decreasing this makes the plot appear more squat.
`xy_aspectratio`	The aspect ratio for the xy axis compared to z (default = 1). Decreasing this makes the grid wider in the plot window.
`plot_height`	The plot height in px. Default=700.
`...`	Optional parameters to pass to `polar_grid`.

Returns a cylindrical 3D plotly plot featuring variables on a tri-axis radial graph with the -log10(multi-group test p-value) on the z-axis

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_col_suffix='log2FoldChange',
                          fc_cutoff = 0.3)

volcano3D(syn_polar, 
    label_rows = c("FMOD", "LAMP5", "TNNT3"), 
    xy_aspectratio = 1, 
    label_size = 10, 
    z_aspectratio = 0.9)