Generates a manhattan plot of the results of a genome wide association test.

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`p` |
A vector of p-values. |

`chromosome` |
A vector containing the chromosome for each SNP. |

`ylim` |
The limits of the y axis. If NULL, the y axis is |

`trunc.lines` |
Logical value indicating whether to show truncation lines. |

`signif` |
Genome-wide significance level for plotting horizontal
line. If |

`thinThreshold` |
if not |

`pointsPerBin` |
number of points to plot in each bin if |

`col` |
vector containing colors of points; defaults to coloring by chromosome using the colorbrewer Dark2 palette with 8 colors |

`...` |
Other parameters to be passed directly to |

Plots -log10(p) versus chromosome. Point size is scaled so that smaller p values have larger points.

`p`

must have the same length as `chromosome`

and is
assumed to be in order of position on each chromosome. Values within
each chromosome are evenly spaced along the X axis.

Plot limits are determined as follows: if `ylim`

is provided, any
points with `-log10(p) > ylim[2]`

are plotted as triangles at the
maximum y value of the plot. A line will be drawn to indicate
trunctation (if `trunc.lines == TRUE`

, the default). If
`ylim == NULL`

, the maximum y value is defined as
`log10(length(p)) + 4)`

.

If requested with `thinThreshold`

, points with `-log10(pval) < thinThreshold`

are thinned before plotting. All points with `-log10(pval) >= thinThreshold`

are displayed. P-values with `-log10(pval) < thinThreshold`

are sampled such that `pointsPerBin`

points are randomly selected from 10 bins with uniform spacing in `-log10(pval)`

space.

Cathy Laurie, Adrienne Stilp

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