plot.manta {manta} | R Documentation

## Plot a MAnTA object

### Description

A MANTA RAy plot is designed for visualizing comparative meta-transcriptomics, but can be used in any case where fold change data assessment calls for displaying additional meta information.

### Usage

    manta.ra(x, uniques=4, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')),
                           nr=0, alpha = 0.01, normalize=FALSE,
                           meta.level=names(x$meta.sum)[1], meta.lgnd.lim=6, lgd.pos='topright', lgd.cex=.75, lgd.trunk=FALSE, pie.lwd=1,
                           annot=NULL, vrb.axlabs=TRUE, jitter=.43, border='black',
                           rex=2, flat=FALSE, tail=.5, arms=.5, spine=1, ...)

### Arguments

`x` | a MAnTA object.
`uniques` | a boolean specifying whether or not to plot the library-unique genes (those with zero counts in one or the other library).
`pair` | a named vector indicating the condition names and the corresponding the reference or observation status of each.
`nr` | a numeric value indicating the asymptotic normalization ratio line.
`alpha` | a statistical significance value.
`normalize` | A boolean specifying whether or not to normalize the counts into proportions.
`meta.level` | a number or string specifies which taxonomic level (which meta list element) should be used to generate the pie charts. 0 or FALSE indicates no pies should be drawn.
`meta.lgnd.lim` | an integer specifying the top n most common taxonomic levels to use in the pies and legend.
`lgd.pos` | a string specifying the general position of the legend (see the legend function documentation).
`lgd.trunk` | a boolean specifying if the legend should trunkate (for example) Genus species to G.species
`lgd.cex` | a numeric value specifying the character expansion for the legend text.
`pie.lwd` | the line thickness of the pie polygon border.
`annot` | a named vector of strings that match which points should be annotated in the plot. names indicate the colors of the text.
`vrb.axlabs` | a boolean indicating if verbose axis labels should be use to spell out exactly how the axes are calculated.
`jitter` | whether or not or how much to jitter the counts into surrounding, non-overlapping space.
`rex` | a numeric value specifying the radial expansion of the plot points.
`flat` | a boolean for the radial expansion of points as a function of both R and A axes.
`tail` | a numeric or boolean value indicating the line thickness of the two trailing curved significance lines of the RAy.
`arms` | a numeric or boolean value indicating the line thickness of the two leading straight separator lines of the RAy.
`spine` | a numeric or boolean value indicating the line thickness of the normalization line (whose y position is specified by mm).
`border` | a vector of strings used to color the borders of the points.
`...` | other parameters passed to plot.

### Value

A MAnTA RAy plot.

### See Also

maPlot, plotMA, raPlot, pies

### Examples

    manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
    load(manta.path)
    plot(x, meta.lev='genus_sp')

[Package manta version 1.26.0 Index]