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

Given a `filterObject`

and a `datasetObject`

this function will use the selected genes of the `filterObject`

to calculate and compare the z-scores of the groups (e.g. cases vs. controls) from the `datasetObject`

by generating a violin plot. A violin plot is similar to a box plot, except the width of each violin is proportional to the density of points. `violinPlot()`

is commonly used to validate a gene signature in an independent dataset.

1 2 3 | ```
violinPlot(filterObject, datasetObject, labelColumn = "label",
comparisonMethod = "wilcox.test", pairwiseComparisons = TRUE,
autoLineBreak = TRUE)
``` |

`filterObject` |
a MetaFilter object containing the signature genes that will be used for the z-score calculation |

`datasetObject` |
a Dataset object (typically independent validation dataset) for group comparison in a violin plot |

`labelColumn` |
the label of the column in |

`comparisonMethod` |
statistical test that will be used (default="wilcox.test"). Other options include "t.test". |

`pairwiseComparisons` |
if TRUE, perform pairwise statistical comparisons against the first factor level. If FALSE, perform global statistical comparisons (default: TRUE). |

`autoLineBreak` |
if TRUE, insert line breaks into labels on plots. If FALSE, don't insert line breaks (default: TRUE) |

The z-score is based off of the geometric mean of expression. As such, negative expression values are not allowed. A dataset is thus always scaled by its minimum value + 1, such that the lowest value = 1. Any individual NANs or NAs are also set to 1. If a dataset does not have any information on a given gene, the entire gene is simply left out of the score.

Returns a violin plot as ggplot2 plot object

Winston A. Haynes

1 2 3 | ```
violinPlot(tinyMetaObject$filterResults$pValueFDR0.05_es0_nStudies1_looaTRUE_hetero0,
tinyMetaObject$originalData$Whole.Blood.Study.1,
labelColumn="group")
``` |

```
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.