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
|
filter_for |
String. Must either be |
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 leastthreshold
times.If neither
top
northreshold
is given,top
is automatically set to5
.
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
Other target functions:
count_target()
,
join_mirtarbase()
,
join_targets()
,
plot_target_count()