manta (version 1.18.0)

plot.manta: 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')