Description Usage Arguments Details Author(s) Examples

Displays a correlation circle of a multivariate analysis.

1 2 3 4 5 6 7 | ```
MVA.corplot(x, xax = 1, yax = 2, thresh = 0, fac = NULL, set = c(12, 1, 2), space = 1,
xlab = NULL, ylab = NULL, main = NULL, circle = TRUE, intcircle = 0.5, points = TRUE,
ident = TRUE, arrows = TRUE, labels = NULL, main.pos = c("bottomleft", "topleft",
"bottomright", "topright"), main.cex = 1.3, legend = FALSE, legend.pos = c("topleft",
"topright", "bottomleft", "bottomright"), legend.title = NULL, legend.lab = NULL,
pch = 16, cex = 1, col = 1, lwd = 1, drawintaxes = TRUE, add = FALSE, add.const = 1,
keepmar = FALSE)
``` |

`x` |
a multivariate analysis (see Details). |

`xax` |
the horizontal axis. |

`yax` |
the vertical axis. This can be set to |

`thresh` |
threshold (in absolute value of the correlation coefficient) of variables to be plotted. |

`fac` |
an optional factor defining groups of variables. |

`set` |
variables to be displayed, when several sets are available (see Details). |

`space` |
variables to be displayed, when several spaces are available (see Details). |

`xlab` |
legend of the horizontal axis. If |

`ylab` |
only used for two-dimensional graphs. Legend of the vertical axis. If |

`main` |
optional title of the graph. |

`circle` |
only used for two-dimensional graphs. Logical indicating if the circle of radius 1 should be plotted. |

`intcircle` |
only used for two-dimensional graphs. Vector of one or several values indicating radii of circles to be plotted inside the main circle. Can be set to |

`points` |
only used for two-dimensional graphs. If |

`ident` |
only used for two-dimensional graphs when |

`arrows` |
only used if |

`labels` |
names of the variables. If |

`main.pos` |
position of the title, if |

`main.cex` |
size of the title, if |

`legend` |
only used for two-dimensional graphs. Logical indicating if a legend should be added to the graph. |

`legend.pos` |
position of the legend, if |

`legend.title` |
optional title of the legend, if |

`legend.lab` |
legend labels, if |

`pch` |
symbol(s) used for points, when points are displayed (see |

`cex` |
size of the points and/or of the variable names. For two-dimensional graphs: if |

`col` |
color(s) used for points and/or variable names. If |

`lwd` |
only used if arrows are displayed. Width of arrows. If |

`drawintaxes` |
logical indicating if internal axes should be drawn. |

`add` |
only used for two-dimensional graphs. Logical indicating if the correlation circle should be added to an existing graph. |

`add.const` |
only used for two-dimensional graphs and if |

`keepmar` |
only used for two-dimensional graphs. Logical indicating if margins defined by MVA.corplot should be kept after plotting (necessary in some cases when |

This function should not be use directly. Prefer the general `MVA.plot`

, to which all arguments can be passed.

Many multivariate analyses are supported, from various packages:

- PCA: `dudi.pca`

, `rda`

.

- sPCA: `spca`

.

- IPCA: `ipca`

.

- sIPCA: `sipca`

.

- LDA: `lda`

, `discrimin`

.

- PLS-DA (PLS2 on a dummy-coded factor): `plsda`

. X space only.

- sPLS-DA (sPLS2 on a dummy-coded factor): `splsda`

. X space only.

- CPPLS: `mvr`

. Set 1 is X, set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set. X space only.

- PLSR: `mvr`

, `pls`

, `plsR`

(plsRglm package). Set 1 is X, set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set. X space only.

- sPLSR: `pls`

. Set 1 is X, set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set. X space only.

- PLS-GLR: `plsRglm`

(plsRglm package). Set 1 is X, set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set. Correlations are computed with Y on the link scale.

- PCR: `mvr`

. Set 1 is X, set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set.

- CDA: `discrimin`

, `discrimin.coa`

.

- NSCOA: `dudi.nsc`

. For NSCOA there is no real correlation, but the classical representation of columns is arrows. This is why MVA.corplot was made able to deal with this analysis.

- CCA: `cca`

, `pcaiv`

. Constraints (only quantitative constraints are extracted) in constrained space only.

- Mix analysis: `dudi.mix`

, `dudi.hillsmith`

. Only quantitative variables are displayed.

- RDA (or PCAIV): `pcaiv`

, `pcaivortho`

, `rda`

. With `rda`

, space 1 is constrained space, space 2 is unconstrained space. Only constrained space is available with `pcaiv`

, the opposite for `pcaivortho`

. Set 1 is constraints (only quantitative constraints are extracted), set 2 is dependent variables (only set 2 is available for `pcaivortho`

). If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set.

- db-RDA: `capscale`

, `dbrda`

. Constraints (only quantitative constraints are extracted) in constrained space only.

- CCorA: `CCorA`

, `rcc`

. Space 1 is X, space 2 is Y. With `rcc`

a third space is available, in which coordinates are means of X and Y coordinates. In this third space, set 1 is X, set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set.

- rCCorA: `rcc`

. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates. In space 3, set 1 is X and set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set.

- CIA: `coinertia`

. Space 1 is X, space 2 is Y, space 3 is a "common" space where X and Y scores are normed. In space 3, set 1 is X and set 2 is Y. If `set=12`

in space 3 (default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lws`

can be defined differently for each set.

- PCIA: `procuste`

. Set 1 is X, set 2 is Y.

- 2B-PLS: `pls`

. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates. In space 3, set 1 is X and set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set.

- 2B-sPLS: `pls`

. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates. In space 3, set 1 is X and set 2 is Y. If `set=12`

(default), `fac`

is not available and `pch`

,`cex`

, `col`

, `lwd`

can be defined differently for each set.

- rGCCA: `wrapper.rgcca`

. Space can be 1 to n, the number of blocks (i.e. datasets).

- sGCCA: `wrapper.sgcca`

. Space can be 1 to n, the number of blocks (i.e. datasets).

- DIABLO: `block.plsda`

, `block.splsda`

. Space can be 1 to n, the number of blocks (i.e. datasets).

Maxime Herv<e9> <[email protected]>

1 2 3 4 |

RVAideMemoire documentation built on May 14, 2018, 5:07 p.m.

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