Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function takes a `ICMatrix`

or `TFFM`

object
and plot the sequence logo.

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`x` |
x is a valid |

`ic.scale` |
A logical value. If TRUE, the total height of one column is proportional to the information content at that position. Otherwise, all the columns will have the same height. Ignored for |

`xaxis` |
A logical value. If TRUE, the x-axis will be plotted. Ignored for |

`yaxis` |
A logical value. If TRUE, the y-axis will be plotted. Ignored for |

`xfontsize` |
A numeric value. The font size for x-axis. |

`yfontsize` |
A numeric value. The font size for y-axis. |

A sequence logo is a graphical representation of the matrix model,
based on the information content of each position.
The information content ranges from 0 (no base preference) to 2 (only 1 base used).
If `ic.scale`

is TRUE,
the height of the logo at certain site is proportinal to
the information content value.
And each stacked base (A, C, G, T)'s height is also proportional to
the information content of each base at that position,
and sorted based on the character size.

For a `TFFM`

object, a novel graphical representation is used for
capturing the dinucleotide dependencies on the TFFM.
For the upper part of the sequence logo,
we represent the nucleotide probabilities
at position p for each possible nucleotide at position p-1.
Hence, each column represents a position within a TFBS and
each row the nucleotide probabilities found at that position.
Each row assumes a specific nucleotide has been emitted
by the previous hidden state.
The intersection between a column corresponding to position p and
row corresponding to nucleotide n gives the probabilities of
getting each nucleotide at position p if n has been seen at position p-1.
The opacity to represent the sequence logo is proportional to
the probablity of
possible row to be used by the TFFM.

No return value.

This function is based on the function `seqLogo`

from the Bioconductor
package `seqLogo`

, especially for the plotting code of TFFM.

Ge Tan

T D Schneider, R. M. S. (1990). Sequence logos: a new way to display consensus sequences. Nucleic acids research, 18(20), 6097.

Mathelier, A., and Wasserman, W.W. (2013). The next generation of transcription factor binding site prediction. PLoS Comput. Biol. 9, e1003214.

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