diffLogoTableConfiguration {DiffLogo} | R Documentation |
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 |
list of parameters
Lando Andrey
diffLogoTableConfiguration(DNA)