metamicrobiomeR (version 1.2)

metatab.show: Display meta-analysis results.

Description

This function displays meta-analysis results of relative abundance as heatmap, forest plot, table or data.

Usage

metatab.show(
  metatab,
  com.pooled.tab,
  sumvar = "taxa",
  highest.lev = "g",
  tax.lev = "l2",
  showvar,
  estimate.pattern = "Estimate.",
  se.pattern = "Std. Error.",
  p.pattern = "Pr(>|t|)",
  readjust.p = FALSE,
  p.cutoff.type = "p",
  p.cutoff = 0.05,
  display = "plot",
  plot = "heatmap",
  fill.value = "log(OR)",
  grid = FALSE,
  digit = 2,
  p.digit = 4
)

Arguments

metatab

matrice of taxa/pathway abundance comparison meta-analysis results generated from meta.taxa.

com.pooled.tab

matrice of taxa/pathway abundance comparison generated from taxa.compare or pathway.compare combined from all included studies.

sumvar

Either "taxa" for taxa and "path" for pathway.

highest.lev

Highest level of bacterial taxonomies available for analysis. Options are "g" for genus (usually for 16S data) and "s" for species (usually for shortgun data).

tax.lev

taxa level to be displayed. Options are from "l2" (phylum) to "l7" (species). Default is "l2".

showvar

variable (string pattern) in the model to be displayed.

estimate.pattern

string pattern for estimates. Default is "Estimate.".

se.pattern

string pattern for standard error variable. Default is "Std. Error.".

p.pattern

string pattern for p-value variable. Default is "Pr(>|t|)".

readjust.p

multiple testing re-adjustment for only the level to be displayed (TRUE) or keep original multiple testing adjustment for all taxa of all levels (FALSE).Default is FALSE.

p.cutoff.type

type of p-value for cutoff. Options are "p" for p-value or "p.adjust" for multiple testing adjusted p-value. Default is "p".

p.cutoff

cutoff p-value to be displayed. Default is 0.05.

display

type of display. Options are display=c("plot","table","data")

plot

type of plot. Options are plot=c("heatmap","forest").

fill.value

name of legend.

grid

whether multiple plots will be displayed alongside. Default is FALSE.

digit

digit for estimates and 95 CI. Default is 2.

p.digit

digit for p-values. Default is 4.

Value

plot table or data.

Examples

# NOT RUN {
# Load saved GAMLSS-BEZI results of four studies for the comparison of
# bacterial taxa relative abundance between genders adjusted for
# breastfeeding and infant age at sample collection
data(tabsex4)
#select only taxonomies of a small phylum for meta-analysis example
# (to save running time)
tlm<-tabsex4$id[grep("k__bacteria.p__fusobacteria",tabsex4$id)]
# meta-analysis
metab.sex<-meta.taxa(taxcomdat=tabsex4[tabsex4$id %in% tlm,],
summary.measure="RR", pool.var="id", studylab="study",
backtransform=FALSE, percent.meta=0.5, p.adjust.method="fdr")
#show results by table and plot
#phylum
#table
metatab.show(metatab=metab.sex$random,com.pooled.tab=tabsex4[tabsex4$id %in% tlm,],
tax.lev="l2",showvar="genderMale",p.cutoff.type="p", p.cutoff=1,display="table")
#plot
metadat<-metatab.show(metatab=metab.sex$random,com.pooled.tab=tabsex4[tabsex4$id %in% tlm,],
tax.lev="l2",showvar="genderMale",p.cutoff.type="p", p.cutoff=1,display="data")
meta.niceplot(metadat=metadat,sumtype="taxa",level="main",p="p",
p.adjust="p.adjust",phyla.col="rainbow",p.sig.heat="yes",
heat.forest.width.ratio =c(1.5,1), leg.key.size=0.8,
leg.text.size=10, heat.text.x.size=10, heat.text.x.angle=0,
forest.axis.text.y=8,forest.axis.text.x=10,
point.ratio = c(4,2),line.ratio = c(2,1))
# }