The tornado_plot() function exists to easily jot down a tornado plot. The
idea behind this function is that whenever you're in doubt on how to plot
your tornado data, this is the function that tries to figure it out for you.
A TornadoExperiment, tornado_df or other type of
data forwarded to build_tornado().
...
Arguments passed on to build_tornado, prep_tornado, autoplot.tornado_df
features
A GRanges or GRangesList object
containing genomic loci of interest.
width
An integer(1) in basepairs with respectively a
common feature width to centre features in, a size of bins to summarise
coverage in or the number of bins to summarise coverage in. Only two of
these need to be defined.
binwidth
An integer(1) in basepairs with respectively a
common feature width to centre features in, a size of bins to summarise
coverage in or the number of bins to summarise coverage in. Only two of
these need to be defined.
nbin
An integer(1) in basepairs with respectively a
common feature width to centre features in, a size of bins to summarise
coverage in or the number of bins to summarise coverage in. Only two of
these need to be defined.
pad_value
A numeric(1) to use for padding when
seqlenghts(features) are unknown or
features exceed known sequence lengths.
assay_name
A character(1): one of the assay names retrieved by
assayNames(tornado).
upper
Limits to the colour scale. Can be one of the following:
A numeric to set absolute limits directly.
A character in the form of a number prefixed by "p" or "q" to set
the percentile or quantile respectively. For example, "p99" and "q0.95"
set the limit to the 99th percentile or 0.95th quantile respectively. The
limits as specified in the lower and upper arguments can be overridden
if the scale argument has non-default limits.
lower
Limits to the colour scale. Can be one of the following:
A numeric to set absolute limits directly.
A character in the form of a number prefixed by "p" or "q" to set
the percentile or quantile respectively. For example, "p99" and "q0.95"
set the limit to the 99th percentile or 0.95th quantile respectively. The
limits as specified in the lower and upper arguments can be overridden
if the scale argument has non-default limits.
scale_title
A character(1) with the title for the colourbar. Can
be overridden when the scale argument has a non-default name.
scale
A continuous fill scale from
the ggplot2 package to use to colour the tornado. When NULL (default),
the scale will be retrieved from the option "tornadoplot.default.scale".
facet
A logical(1) or ggplot2 facet. If TRUE, a
facet_tornado() is added. If FALSE, no facet will
be added. When a ggplot2 facet, the facet is added to the plot.
x_scale
A logical(1) or ggplot2 x scale. If TRUE, an x scale is
added that attempts to avoid overlapping labels.
y_scale
A logical(1) or ggplot2 y scale. If TRUE, a y scale is
added that marks regular intervals but only labels the number of features.
sort
A logical(1). Should the tornado be sorted from high to low?
Does not apply for the tornado_df method.
Value
Prints a plot as a side effect. Returns a TornadoExperiment with
the plot in the metadata() slot. When
data is a tornado_df object, instead it returns the plot as-is.
Methods (by class)
ANY: The ... argument is forwarded to
build_tornado().
TornadoExperiment: The ... argument is forwarded to
prep_tornado().
tornado_df: The ... argument is forwarded to
autoplot().
Examples
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# These features and data aren't really prettyfeats<-dummy_features()data<-dummy_granges_data()# This will extract and plot the data. The extracted data is now stored in x.x<-tornado_plot(data,features=feats,width=3000)# `x` is the data underlying the plot in an TornadoExperiment object.print(x)# The plot generated above is stored in the metadatametadata(x)$plot# Or the plot can be recomputed from the datatornado_plot(x)
