Description Usage Arguments Details Value Examples

Convert P-values to color index

1 | ```
convertPvalueToColorIndex(p.vals, scale="auto", max.color.index, minimal.p.value=1e-04)
``` |

`p.vals` |
the P-values (after any multiple testing correction) |

`scale` |
the color is calculated liked -log10( p.value) * scale, thus scale is used to scale the -log10 to the desired range. Either a number or "auto" for automatic |

`max.color.index` |
the maximal color index to return |

`minimal.p.value` |
the minimal P-value we accept (since from Monte Carlo we can get 0) |

Convert p values to a color index to color nodes in a graph. The P-values are fit into a range from 1 to
`max.color.index`

by applying a scale. Before fitting, P-value are transformed by taking a log10,
and a minimal P-value is needed to avoid -Inf results for very small P-values. Scale can either be a number
or "auto" in which case color coding is such that all P-values fit into the range.

a `list`

with following elements: `col`

- the color indexes, `zlim`

- the
actual scale range (in log10) over the colors

1 2 | ```
# scale the P values into the log10 space of [1e-3,1] represented by max 6 colours
convertPvalueToColorIndex(c(0.01, 0.2, 0.3), scale="auto", max.color.index=6, minimal.p.value=1e-3)
``` |

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