Plots the three-way comparisons of variables such as gene expression data in 3D space using plotly. x, y position represents polar position on 3 axes representing the amount each variable or gene tends to each of the 3 categories. The z axis represents -log10 P value for the one-way test comparing each variable across the 3 groups.

volcano3D(
polar,
type = 1,
label_rows = c(),
label_size = 14,
arrow_length = 100,
colour_code_labels = FALSE,
label_colour = "black",
grid_colour = "grey80",
grid_width = 2,
grid_options = NULL,
axis_colour = "black",
axis_width = 2,
marker_size = 3,
marker_outline_width = 0,
marker_outline_colour = "white",
z_axis_title_offset = 1.2,
z_axis_title_size = 12,
z_axis_angle = 0.5,
xy_aspectratio = 1,
z_aspectratio = 0.8,
camera_eye = list(x = 0.9, y = 0.9, z = 0.9),
...
)

Arguments

polar Object of S4 class 'volc3d' following call to either polar_coords, deseq_polar or voom_polar Either 1 or 2 specifying type of polar coordinates: 1 = Z-scaled, 2 = unscaled (equivalent to log2 fold change for gene expression). A vector of row names or numbers to label font size for labels (default 14). The length of label arrows (default 100) Logical whether label annotations should be colour coded. If FALSE label_colour is used. HTML colour of annotation labels if not colour coded. The colour of the cylindrical grid (default "grey80") The width of the grid lines (default 2) Optional list of additional arguments to pass to polar_grid, eg. z_axis_ticks and r_axis_ticks The colour of the grid axes and labels (default "black") The width of axis lines (default 2) Size of the markers (default 3) Width for marker outline (default 0 means no outline) Colour for marker outline (default white) The position scaling between grid and z axis title (default=1.2) The font size for the z axis title (default=12) Angle in radians for the position of z axis (default 0.5) The font size for the radial (default=15) The position scaling between grid and radial axis title (default=1.2) The aspect ratio for the xy axis compared to z (default 1). Increasing this makes the grid wider in the plot window. The aspect ratio for the z axis compared to x and y (default 0.8). Decreasing this makes the plot appear more squat. The (x,y,z) components of the start 'eye' camera vector. This vector determines the view point about the origin of this scene. Optional arguments passed to plot_ly

Value

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

References

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

polar_coords
data(example_data)