bbplot2d: Plot of metapone result.

In tianwei-yu/metapone: Conducts pathway test of metabolomics data using a weighted permutation test

Plot of metapone result.

Description

The function bbplot2d() select important pathways with their P-value less than a threshold and returns a 2-D bubble plot with -log10(Pvalue) and the number of significant metabolites as coordinate axes.

Usage

bbplot2d(res, p_thres = 0.05, sig_metab_thres = 1, low.color = "MidnightBlue", high.color = "LightSkyBlue")

Arguments

res	The result matrix obtained from metapone with columns: "p_value", "n_significant metabolites", "n_mapped_metabolites", "n_metabolites", "significant metabolites", "mapped_metabolites", "fdr".
p_thres	The threshold of P-value for pathways to be shown in the bubble plot. The default threshold is 0.05.
sig_metab_thres	The threshold of fractional matched significant metabolite count for pathways to be shown in the bubble plot. The default is 1.
low.color	The GRB color of the lowest ldfr value to be shown in the bubble plot.
high.color	The GRB color of the highest ldfr value to be shown in the bubble plot.

Author(s)

Leqi Tian ([e-mail])

See Also

metapone

Examples

data(hmdbCompMZ.metapone)
data(pa)
data(pos)
data(neg)
dat <- list(pos, neg)
type <- list("pos", "neg")
r<-metapone(dat, type, pa, hmdbCompMZ=hmdbCompMZ.metapone, p.threshold=0.05,
   n.permu=100,fractional.count.power=0.5, max.match.count=10)
bbplot2d(ptable(r)) # p_thres = 0.05

tianwei-yu/metapone documentation built on Aug. 21, 2022, 3:09 a.m.