View source: R/polyqtlR_functions.R

plotRecLS | R Documentation |

Function which visualises the recombination landscape in two ways: per linkage group, and per individual.
For the first analysis, a rudimentary spline is also fitted to estimate the recombination rate along a grid of positions defined by `gap`

,
which is also returned by the function.

```
plotRecLS(
recombination_data,
plot_per_LG = TRUE,
plot_per_ind = TRUE,
gap = 1,
...
)
```

`recombination_data` |
Data on predicted recombination events, as returned by the function |

`plot_per_LG` |
Logical argument, plot recombination events per linkage group? By default |

`plot_per_ind` |
Logical argument, plot recombination events per individual? By default |

`gap` |
The size (in cM) of the gap used to define the grid of positions to define the window in which to estimate recombination rate. By default 1 cM. Interpolated positions are taken to be the centre of an interval, so a 1 cM gap would result in predictions for positions 0.5 cM, 1.5 cM etc. |

`...` |
Option to pass extra arguments to the |

A list with two elements, `per_LG`

and `per_individual`

. The first of these is itself a list with the same length as `recombination_data`

, giving the estimated recombination rates along the linkage group.
This rate is simply estimated as the (weighted) count of recombination breakpoints divided by the population size.

```
data("Rec_Data_4x")
plotRecLS(Rec_Data_4x)
```

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