plot.positions

plot.positions-method

plot.positions,cobindr-method


    an object of the class "cobindr", which will hold all necessary
    information about the sequences and the hits.



    list of sequence identifiers, for which the positions of TFBS will
    be plotted.


seq.ids


    list of PWMs, for which the positions will be visualized. If no list
    is given, all PWMs in runObj are used.


pwms


    title for the plot, if no title is given than 'predicted TFBS
    positions per sequence' will be used


main


    logical flag, if TRUE similar patterns of TFBS are shown
    together. This is computationally expensive for large numbers of sequences.


order.seq


    integer describing the windows which will be used to enhance
    clustering of TFBS patterns. Necessary if order.seq=TRUE


wind.size

frac


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.


 hplot

 dplot 

Finding and analysing co-occuring motifs of transcription
factor binding sites in groups of genes

Manuela Benary

cobindR

Finding Co-occuring motifs of transcription factor binding sites