plot_target_mir_scatter: Plot targets and corresponding miRNAs as a scatter plot

In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

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

Scatter plot with targets and corresponding miRNAs.

See Also

join_targets()

Other target functions: count_target(), join_mirtarbase(), join_targets(), plot_target_count()

JulFriedrich/miRetrieve documentation built on Sept. 20, 2021, 11:37 p.m.