Description Usage Arguments Value Author(s) Examples

Draws the difference of two sequence logos.

1 2 3 4 5 6 7 | ```
diffLogoFromPwm(pwm1, pwm2, ymin = 0, ymax = 0,
stackHeight = shannonDivergence,
baseDistribution = normalizedDifferenceOfProbabilities, sparse = FALSE,
alphabet = DNA, align_pwms = FALSE,
unaligned_penalty = divergencePenaltyForUnaligned,
try_reverse_complement = TRUE, base_distribution = NULL,
length_normalization = FALSE)
``` |

`pwm1` |
representation of the first position weight matrix (PWM) of type pwm, data.frame, or matrix |

`pwm2` |
representation of the second position weight matrix (PWM) of type pwm, data.frame, or matrix |

`ymin` |
minimum value on the y-axis |

`ymax` |
maximum value on the y-axis |

`stackHeight` |
function for the height of a stack at position i |

`baseDistribution` |
function for the heights of the individual bases |

`sparse` |
if TRUE margins are reduced and tickmarks are removed from the logo |

`alphabet` |
of type Alphabet |

`align_pwms` |
if true, DiffLogo will align pwms before plotting |

`unaligned_penalty` |
is a function for localPwmAlignment. |

`try_reverse_complement` |
if True, alignment will try reverse complement pwms |

`base_distribution` |
is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used |

`length_normalization` |
If true, will minimize the average divergence between PWMs. Otherwise will minimize the sum of divergences between positions. In both cases unalignes positions are compared to base_distribution and are counted when computing the alignment length. |

none (draws difference logo)

Martin Nettling

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
motif_folder= "extdata/pwm"
motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
motifs = list()
for (name in motif_names) {
fileName = paste(motif_folder,"/",name,".pwm",sep="")
file = system.file(fileName, package = "DiffLogo")
motifs[[name]] = getPwmFromPwmFile(file)
}
pwm1 = motifs[[motif_names[[1]]]]
pwm2 = motifs[[motif_names[[2]]]]
diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2)
``` |

DiffLogo documentation built on Nov. 1, 2018, 2:24 a.m.

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