Description Usage Arguments Details Author(s) References Examples

This function creates a scatter plot that is augmented with marginal histograms (with smoothed splines) on the x and y-axes.

1 2 3 4 |

`dat` |
a matrix with rows representing species samples and two columns representing the variables of interest (typically a selected principal component of size and shape variables) |

`seqx` |
range of values on the x-axis, for histogram plotting |

`seqy` |
range of values on the y-axis, for histogram plotting |

`ybound` |
range of values on the y-axis |

`xbound` |
range of values on the x-axis |

`y.label` |
title for y-axis |

`x.label` |
title for x-axis |

`labcol` |
a character vector giving the color annotation for species names in alphabetical order |

`type` |
a character that controls where the marginal histograms are located: right-up ("ru"), left-up ("lu"), left-down ("ld"), right-down ("rd") |

`sep1` |
tick mark separation for x-axis |

`sep2` |
tick mark separation for y-axis |

`phylo` |
if TRUE, the centroids of species are joined into a tree-like object corresponding to their phylogeny given in |

`phy` |
a tree object of class |

`pointscale` |
a constant specifying the symbol size of the centroids |

`supp.hist.y` |
if TRUE, suppresses the plotting of marginal histogram at the y-axis |

`supp.hist.x` |
if TRUE, suppresses the plotting of marginal histogram at the x-axis |

`y.axis.label` |
if FALSE, suppresses the y-axis title |

`x.axis.label` |
if FALSE, suppresses the x-axis title |

`addline` |
an optional numeric vector of length two specifying the intercept and slope of linear line |

This function is similar to `tpColorPlot2d`

, and is mainly useful for its additional
option for visualising the marginal distributions. The `ape`

and `phytools`

packages are required.

Tsung Fei Khang tfkhang@um.edu.my

Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4:e1668.

Paradis E, Claude J & Strimmer K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.

Revell LJ. (2012). phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217-223.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
library(phytools)
data(pwed_pd)
data(ligotree)
data(spcolmap)
#principal component analysis of size variables from ventral and dorsal anchors
pca2d_pwedv <- pca2d(pwed_pd[,1:55], sgn=-1, labcol=spcolmap$color,
phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.2, 0.2),
bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))
pca2d_pwedd <- pca2d(pwed_pd[,56:110], sgn=-1, labcol=spcolmap$color,
phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.2, 0.2),
bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))
#comparing size PC1 between ventral and dorsal anchors
hsplot(cbind(pca2d_pwedv$scores[,1], pca2d_pwedd$scores[,1]),
seqx=seq(-0.2,0.15,0.01), seqy=seq(-0.2,0.15,0.01),
xbound=c(-0.2,0.15), ybound=c(-0.2,0.15), y.label="Dorsal size PC1",
x.label="Ventral size PC1", labcol=spcolmap$color, type="ru",
sep1=0.1, sep2=0.1, phylo=FALSE, addline=c(0,1))
``` |

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