Description Usage Arguments Value Author(s) Examples

View source: R/diffSeqLogoSupport.R

Default configuration list for diffLogoTable

1 2 3 4 5 6 7 8 | ```
diffLogoTableConfiguration(alphabet, stackHeight = shannonDivergence,
baseDistribution = normalizedDifferenceOfProbabilities,
uniformYaxis = TRUE, sparse = TRUE, showSequenceLogosTop = TRUE,
enableClustering = TRUE, treeHeight = 0.5, margin = 0.02,
ratio = 1, align_pwms = FALSE, multiple_align_pwms = TRUE,
unaligned_penalty = divergencePenaltyForUnaligned,
try_reverse_complement = TRUE, length_normalization = FALSE,
numberOfPermutations = 100)
``` |

`alphabet` |
used alphabet of type Alphabet |

`stackHeight` |
function for the height of a stack at position i |

`baseDistribution` |
function for the heights of the individual bases |

`uniformYaxis` |
if TRUE each DiffLogo is plotted with the same scaling of the y-axis |

`sparse` |
if TRUE margins are reduced and tickmarks are removed from the logo |

`showSequenceLogosTop` |
if TRUE the classical sequence logos are drawn above each column of the table |

`enableClustering` |
if TRUE the motifs are reordered, so that similar motifs have a small vertical and horizontal distance in the table |

`treeHeight` |
the height of the plotted cluster tree above the columns of the table; set equal to zero to omit the cluster tree |

`margin` |
the space reseverved for labels |

`ratio` |
the ratio of the plot; this is needed to determine the margin sizes correctly |

`align_pwms` |
if True, will align and extend pwms in each cell of diffLogoTable independently. |

`multiple_align_pwms` |
if True, will align and extend pwms in the diffLogoTable jointly. |

`unaligned_penalty` |
is a function for localPwmAlignment. |

`try_reverse_complement` |
if True, alignment will try reverse complement pwms |

`length_normalization` |
if True, divergence between pwms is divided by length of pwms. |

`numberOfPermutations` |
number of permutations for the permutation test for the calculation of p-values |

list of parameters

Lando Andrey

1 |

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