Description Usage Arguments Value See Also Examples

This function generate a plot for msviper results showing the enrichment of the target genes for each significant master regulator on the gene expression signature

1 2 3 4 5 |

`x` |
msviper object produced by |

`mrs` |
Either an integer indicating the number of master regulators to include in the plot, or a character vector containing the names of the master regulators to include in the plot |

`color` |
Vector of two components indicating the colors for the negative and positive parts of the regulon |

`pval` |
Optional matrix of p-values to include in the plot |

`bins` |
Number of bins to split the vector of scores in order to compute the density color of the bars |

`cex` |
Number indicating the text size scaling, 0 indicates automatic scaling |

`density` |
Integrer indicating the number of steps for the kernel density. Zero for not ploting it |

`smooth` |
Number indicating the proportion of point for smoothing the density distribution. Zero for not using the smoother |

`sep` |
Number indicating the separation from figure and text |

`hybrid` |
Logical, whether the 3-tail approach used for computingthe enrichment should be reflected in the plot |

`include` |
Vector indicating the information to include as heatmap to the right of the msviper plot: expression and activity |

`gama` |
Positive number indicating the exponential transformation for the activity and expression color scale |

`...` |
Given for compatibility to the plot generic function |

Nothing, a plot is generated in the default output device

1 2 3 4 5 | ```
data(bcellViper, package="bcellViper")
sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic
dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations
mra <- msviper(sig, regulon, dnull)
plot(mra, cex=.7)
``` |

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