diffLogoTableConfiguration: Configuration object for diffLogoTable

Description Usage Arguments Value Author(s) Examples

View source: R/diffSeqLogoSupport.R

Description

Default configuration list for diffLogoTable

Usage

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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

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

...

set of parameters passed to the function 'axis' for plotting

Value

list of parameters

Author(s)

Lando Andrey

Examples

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DiffLogo documentation built on Nov. 1, 2018, 2:24 a.m.