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, 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), ... )
| polar | Object of S4 class 'volc3d' following call to either
|
|---|---|
| type | Either |
| 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 |
| 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
|
| 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 |
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(outcome = syn_example_meta$Pathotype, data = t(syn_example_rld)) volcano3D(syn_polar)