diffLogoTableConfiguration {DiffLogo} | R Documentation

## Configuration object for diffLogoTable

### Description

Default configuration list for diffLogoTable

### Usage

    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)

### Arguments

`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

### Value

list of parameters

### Author(s)

Lando Andrey

### Examples

    diffLogoTableConfiguration(DNA)

[Package DiffLogo version 2.12.2 Index]