plot.positions: function to plot hits for each PWM on the individual sequence
In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description Usage Arguments Author(s)

plot.positions plots hits for each PWM on the individual sequence. Which sequences to plot can be specified by providing a list of sequence identifiers seq.ids. Which PWMs to plot can be specified as list of PWMs. The total height of the plot can be adjusted via argument height.

1 2	## S4 method for signature 'cobindr' plot.positions(x, seq.ids, pwms, main, order.seq = FALSE, wind.size = 400, frac = 10)

`x`	an object of the class "cobindr", which will hold all necessary information about the sequences and the hits.
`seq.ids`	list of sequence identifiers, for which the positions of TFBS will be plotted.
`pwms`	list of PWMs, for which the positions will be visualized. If no list is given, all PWMs in runObj are used.
`main`	title for the plot, if no title is given than 'predicted TFBS positions per sequence' will be used
`order.seq`	logical flag, if TRUE similar patterns of TFBS are shown together. This is computationally expensive for large numbers of sequences.
`wind.size`	integer describing the windows which will be used to enhance clustering of TFBS patterns. Necessary if order.seq=TRUE
`frac`	integer