Description Usage Arguments Author(s)

Generates R or Shiny quantile-quantile (Q-Q) plot given (minimally) an observed vector of p values, plotted their -log1 )quantiles against corresponding -log10 quantiles of the uniform distribution.

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`obs` |
vector of pvalues to plot, names of obs can be intepreted as labels |

`highlight` |
vector optional arg specifying indices of data points to highlight (i.e. color red) (default = c()) |

`exp` |
numeric vector, expected distribution. if default (NULL) will plot observed against a uniform distribution Use this if you are expecting a non-uniform distribution. Must be equal in length to obs. (default = NULL) |

`lwd` |
integer, optional, specifying thickness of line fit to data (default = 1) |

`col` |
a vector of strings (colors) equivalent in length to obs, this is the color that will be used for plotting. This is only if plotly = T (default = NULL) |

`col.bg` |
string indicating the color of the background |

`pch` |
integer dot type for scatter plot |

`cex` |
integer dot size for scatter plot |

`conf.lines` |
logical, optional, whether to draw 95 percent confidence interval lines around x-y line |

`max` |
numeric, optional, threshold to max the input p values |

`max.x` |
numeric, max value for the x axis |

`max.y` |
numeric, max value for the y axis |

`label` |
character vector, optional specifying which data points to label (obs vector has to be named, for this to work) |

`plotly` |
toggles between creating a pdf (FALSE) or an interactive html widget (TRUE) |

`annotations` |
named list of vectors containing information to present as hover text (html widget), must be in same order as obs input |

`gradient` |
named list that contains one vector that color codes points based on value, must bein same order as obs input |

`titleText` |
title for plotly (html) graph only |

`subsample` |
numeric (positive integer), number of points to use for plotting, will be taken randomly from the set of obs -> p values |

`key` |
a character that is passed to the plotly function that will link each point to a give value. For example, if key is set to gene_name The ploted points are refered to by thier gene_name. This is useful when integrating with shiny or any other tool that can integrate with plotly plots. |

Marcin Imielinski, Eran Hodis, Zoran Z. Gajic

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