R: Plot targets and corresponding miRNAs as a scatter plot

plot_target_mir_scatter {miRetrieve}

R Documentation

Plot targets and corresponding miRNAs as a scatter plot

Description

Plot targets and corresponding miRNAs as a scatter plot.

Usage

plot_target_mir_scatter(
  df,
  mir = NULL,
  target = NULL,
  top = NULL,
  threshold = NULL,
  filter_for = "target",
  col.target = Target,
  col.mir = miRNA,
  col.topic = Topic,
  col.pmid = PMID,
  title = NULL,
  height = 0.05,
  width = 0.05,
  alpha = 0.6
)

Arguments

`df`	Data frame containing targets and miRNA names.
`mir`	String or character vector. Specifies which miRNAs to plot.
`target`	String or character vector. Specifies which targets to plot.
`top`	Numeric. Specifies number of top targets/miRNA names to be plotted.
`threshold`	Numeric. Specifies how often a target/miRNA name must be in `df` to be plotted.
`filter_for`	String. Must either be `"target"` or `"miRNA"`. Specifies if `threshold`/`top` shall be applied to targets or miRNA names.
`col.target`	Symbol. Column containing miRNA targets.
`col.mir`	Symbol. Column containing miRNA names.
`col.topic`	Symbol. Column containing topic names.
`col.pmid`	Symbol. Column containing PubMed-IDs.
`title`	String. Plot title.
`height`	Double. Specifies height of jitter.
`width`	Double. Specifies width of jitter.
`alpha`	Double. Specifies opacity of points.

Details

Plot targets and corresponding miRNAs as a scatter plot. With filter_for, it can be determined if the focus shall be on the top targets to plot their corresponding miRNAs, or if the focus shall be on the top miRNA names to plot their corresponding targets. What "top targets" or "top miRNA names" mean can be determined via the top and threshold arguments.

If top is given, df is filtered for the most frequent targets/miRNA names.
If threshold is given, data frame is filtered for all targets/miRNA names mentioned at least threshold times.
If neither top nor threshold is given, top is automatically set to 5.

By plotting miRNAs against their targets, it is visualized if one miRNA regulates many targets, or if one target is regulated by many miRNAs. Furthermore, the miRNA-target interactions are labelled according to their topic in col.topic, thereby facilitating comparison of miRNA-target interactions across different topics.

Value