DiffLogo (version 1.2.1)

diffLogoTable: Draw DiffLogo-table

Description

Draws a table of DiffLogos.

Usage

diffLogoTable(PWMs, stackHeight = shannonDivergence, baseDistribution = normalizedDifferenceOfProbabilities, uniformYaxis = TRUE, sparse = TRUE, showSequenceLogosTop = TRUE, enableClustering = TRUE, treeHeight = 0.5, margin = 0.02, ratio = 1, alphabet = DNA, ...)

Arguments

PWMs

a list/vector of position weight matrices (PWMs) each of type pwm, data.frame, or matrix

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

alphabet

of type Alphabet

...

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

Examples

motif_folder= "extdata/pwm"
motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
motifs = list()
for (name in motif_names) {
  fileName = paste(motif_folder,"/",name,".txt",sep="")
  file = system.file(fileName, package = "DiffLogo")
  motifs[[name]] = as.matrix(read.delim(file,header=FALSE))
}

diffLogoTable(motifs)