Description Usage Arguments Author(s) Examples

View source: R/filter_volcano.R

Generate a volcano plot contrasting p-value with fold change (on the log scale), in order to visualize the effect of filtering on overall variance and also assign significance via p-value.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
filter_volcano(
d, p, S,
n1, n2,
alpha, S_cutoff,
cex = 0.5, pch = 19,
xlab = expression(paste(log[2], " fold change")),
ylab = expression(paste("-", log[10], " p")),
cols = c("grey80", "grey50", "black"),
ltys = c(1, 3),
use_legend = TRUE,
...
)
``` |

`d` |
Fold changes, typically on the log scale, base 2. |

`p` |
The p-values |

`S` |
The overall standard deviation filter statistics, i.e., the square roots of the overall variance filter statistics. |

`n1` |
Sample size for group 1. |

`n2` |
Sample size for group 2. |

`alpha` |
Significance cutoff used for p-values. |

`S_cutoff` |
Filter cutoff used for the overall standard deviation in |

`cex` |
Point size for plotting. |

`pch` |
Point character for plotting. |

`xlab` |
Label for x-axis. |

`ylab` |
Label for y-axis. |

`cols` |
A vector of three colors used for plotting. These correspond to filtered data, data which pass the filter but are insignificant, and data pass the filter and are also statistically significant. |

`ltys` |
The induced bound on log-scale fold change is plotted, as is the
significance cutoff for data passing the filter. The |

`use_legend` |
Should a legend for point color be produced? |

`...` |
Other arguments for |

Richard Bourgon <bourgon@ebi.ac.uk>

1 | ```
# See the vignette: Diagnostic plots for independent filtering
``` |

```
```

genefilter documentation built on Jan. 23, 2021, 2:01 a.m.

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