mmds.3D.plot {bios2mds} | R Documentation |

Displays a 3D plot of the active elements and, if present, of supplementary elements, after a metric MDS analysis.

```
mmds.3D.plot(x, project = NULL, title = NULL, axis = c(1:3),
active.type = "s", sup.type = "p", active.size = 2, radius = 0.005,
sup.size = 10, active.col = x$col[,3], sup.col = project$col[,3],
box = TRUE, axes = TRUE, new.plot = TRUE, label = TRUE,
xlim = NULL, ylim = NULL, zlim = NULL, box.lwd = 2,
box.antialias = TRUE, ...)
```

`x` |
an object of class 'mmds', obtained from |

`title` |
a string of characters representing the title of the plot. Default is "Metric MDS". |

`project` |
an object of class 'project', obtained from |

`axis` |
a numeric vector of length three representing the principal components displayed on the plot. Default is c(1:3). |

`active.type` |
an character indicating the symbol of active elements. This should be one of "s" for spheres, "p" for points, "l" for lines, "h" for line segments from z=0 and "n" for none. Default is "s", corresponding to spheres. |

`sup.type` |
an character indicating the symbol of supplementary elements. This should be one of "s" for spheres, "p" for points, "l" for lines, "h" for line segments from z=0 and "n" for none. Default is "p", corresponding to points. |

`active.col` |
a string of characters or character vector representing the color(s) of the active elements. Default is x$col[,3].
It corresponds either to the user-provided colors if the |

`sup.col` |
a string or character vector representing the color(s) of supplementary elements. Default is project$col[,3].
It corresponds either to the user-provided colors if the |

`active.size` |
a numeric value indicating the size of active symbols. Default is 2. |

`sup.size` |
a numeric value indicating the size of supplementary symbols. Default is 20. |

`box` |
a boolean indicating whether the box should be displayed (TRUE) or not (FALSE). Default is TRUE. |

`axes` |
a boolean indicating whether axes should be displayed (TRUE) or not (FALSE). Default is TRUE. |

`radius` |
a numeric value indicating the radius of spheres symbols only. If x.type equal to "s" the x.size parameter was inactivated. Default is 0.01. |

`new.plot` |
a boolean indicating whether a new 3D plot create/replace active 3D device (TRUE) or not to insert in it (FALSE). Default is TRUE. |

`label` |
a boolean indicating whether the label axes should be displayed (TRUE) or not (FALSE). Default is TRUE. |

`xlim` |
a numeric vector representing the range for the x values. Default is full range. |

`ylim` |
a numeric vector representing the range for the y values. Default is full range. |

`zlim` |
a numeric vector representing the range for the z values. Default is full range. |

`box.lwd` |
a numeric value indicating the width of box and axes lines. Default is 2. |

`box.antialias` |
a boolean specifying if box and axes lines should be antiliased. Default is TRUE. |

`...` |
additional parameters which will be passed to |

If `mmds.3D.plot`

is used after the `col.group`

function,
the elements are colored by the color scheme provided in the .csv file (see `col.group`

for details).
If the `col.group`

function has not been used, the default colors are black and magenta for active and supplementary elements.

`mmds.3D.plot`

helps identify patterns in data and compare active and supplementary elements.

Produces a 3D plot on graphical device.

`mmds.3D.plot`

requires `plot3D`

function from `rgl`

package.
See `rgl`

documentation to supplementary function like `snapshot3D`

to save image file of 3D device.

Jean-Michel Becu

```
# 3D plot of human GPCRs onto the first three axes obained from MDS analysis
# with projection of GPCRs from D. melanogaster as supplementary elements:
data(gpcr)
mmds.3D.plot(gpcr$mmds$sapiens.active,active.type="p",label=FALSE,lit=FALSE,
point_antialias=TRUE,box.lwd=3,sup.size=4.3,active.size=4.3)
bbox3d(shininess=0.5)
```

[Package *bios2mds* version 1.2.3 Index]