Description Usage Arguments Details Value See Also Examples

Construct a new BioSSA decomposition object from passed embryo object or formula.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
## S3 method for class 'formula'
BioSSA(x, data = NULL, ...)
## S3 method for class 'embryo2d'
BioSSA(x,
...,
step = 0.5,
L = c(50, 50),
xlim = c(-Inf, Inf),
ylim = c(-Inf, Inf),
xperc = c(0, 100),
yperc = c(0, 100),
units = c("percent", "original"))
## S3 method for class 'embryo3d'
BioSSA(x, ..., sweep = sweep.function)
``` |

`x` |
formula or object of class ‘embryo2d’ or ‘embryo3d’ |

`...` |
further arguments passed to |

`units` |
units for |

`L` |
vector of two elements, window length (in ‘units’) |

`step` |
grid step for interpolation (in ‘units’) |

`xlim, ylim` |
numeric vectors of two elements, cutoff bounds by AP and DV axes (in ‘units’) |

`xperc, yperc` |
numeric vectors of two elements, denote the size (width and height) of presented embryo part in percent (usefull if data present only a part of the whole embryo) |

`data` |
a data frame (or more precisely, anything that is a valid |

`sweep` |
sweeping function for planarize 3d embryo to 2d ones.
Just now is only default function ( |

For the ‘formula’: formula is evaluated with using `data`

.
The specified data are transformed to ‘embryo2d’ or ‘embryo3d’ object (it's determined by formula length).
the obtained object is passed (along with arguments specified by ...) to the `BioSSA`

method for
corresponding class.

For the ‘embryo3d’ object: 2d projection is performed (using `sweep`

function, topology is kept,
that is, along Y (DV) axis the circulat topology is considered. Thus, ‘embtyo3d’ contains
‘embryo2d’ object. Then the `BioSSA`

method for ‘embryo2d’ class is called.

For the ‘embryo2d’ object: the linear interpolation (see `interp`

)
is performed to the regular grid with step `step`

.
For regular data, the conventional 2D-SSA procedure (`ssa`

from ‘Rssa’) is called.

‘embryo2d’ or ‘embryo3d’ object, according to the type of `x`

,
stores the result of decomposition of the trajectory matrix.
To obtain the decomposition of the data, `reconstruct`

should be called.

BioSSA-class,
`reconstruct`

,
`ssa`

,
`plot.ssa`

.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
xlim <- c(22, 88)
ylim <- c(32, 68)
L <- c(15, 15)
file <- system.file("extdata/data", "ab16.txt", package = "BioSSA")
df <- read.emb.data(file)
bss <- BioSSA(cad ~ AP + DV, data = df, ylim = ylim, xlim = xlim, L = L)
summary(bss)
plot(bss)
plot(bss, type = "ssa-vectors")
plot(bss, type = "ssa-vectors", vectors = "factor")
``` |

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