manta (version 1.18.0)

generateWeights: Generate Weights

Description

Because the manta plot uses integer count data, many of the points overlap and hide a large portion of the data. This function allows one to apply a weighting scheme to jitter points out from under each other both to show the density and expose the content of their pies (if applicable).

Usage

generateWeights(x, w.clmn,  agg.clmn, cond.clmn, ct.clmns=NULL)

Arguments

x

an alignment dataframe

w.clmn

a string corresponding to a column with weight data

agg.clmn

a string corresponding to a column with an aggregation index.

cond.clmn

a string corresponding to a column with condition factor

ct.clmns

a string corresponding to a column with count data

Value

a 2 by n weight matrix

See Also

manta

Examples

align.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.tab", package="manta")
a <- read.delim(align.path, stringsAsFactors=FALSE)
w <- generateWeights(a, 'what_e_value', 'what_def', 'treatment')