volcano3D {volcano3D}

Three-Dimensional Volcano Plot

Description

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.

Usage

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,
  radial_axis_title_size = 14,
  radial_axis_title_offset = 1.2,
  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

type

Either 1 or 2 specifying type of polar coordinates: 1 = Z-scaled, 2 = unscaled (equivalent to log2 fold change for gene expression).

label_rows

A vector of row names or numbers to label

label_size

font size for labels (default 14).

arrow_length

The length of label arrows (default 100)

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")

grid_width

The width of the grid lines (default 2)

grid_options

Optional list of additional arguments to pass to polar_grid, eg. z_axis_ticks and r_axis_ticks

axis_colour

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

axis_width

The width of axis lines (default 2)

marker_size

Size of the markers (default 3)

marker_outline_width

Width for marker outline (default 0 means no outline)

marker_outline_colour

Colour for marker outline (default white)

z_axis_title_offset

The position scaling between grid and z axis title (default=1.2)

z_axis_title_size

The font size for the z axis title (default=12)

z_axis_angle

Angle in radians for the position of z axis (default 0.5)

radial_axis_title_size

The font size for the radial (default=15)

radial_axis_title_offset

The position scaling between grid and radial axis title (default=1.2)

xy_aspectratio

The aspect ratio for the xy axis compared to z (default 1). Increasing this makes the grid wider in the plot window.

z_aspectratio

The aspect ratio for the z axis compared to x and y (default 0.8). Decreasing this makes the plot appear more squat.

camera_eye

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

See Also

polar_coords

Examples

data(example_data)
syn_polar <- polar_coords(outcome = syn_example_meta$Pathotype,
                          data = t(syn_example_rld))
volcano3D(syn_polar)