diffLogoTableConfiguration: Configuration object for diffLogoTable
In mgledi/DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description Usage Arguments Value Author(s) Examples

Default configuration list for diffLogoTable

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