meta.niceplot {metamicrobiomeR}

Nice meta-analysis plots.

Description

This function displays meta-analysis results of relative abundance as a nice combined heatmap and forest plot. More flexibility/options for plot will be added.

Usage

meta.niceplot(
  metadat,
  sumtype = "taxa",
  level = "main",
  p,
  p.adjust,
  phyla.col = "rainbow",
  phyla.select = c("actinobacteria", "bacteroidetes", "cyanobacteria", "firmicutes",
    "fusobacteria", "proteobacteria", "verrucomicrobia", ".thermi."),
  col.select = c("#dd1c77", "#31a354", "#91003f", "#d95f0e", "#636363", "#2ef0e7",
    "#862ef0", "#000"),
  est.break = c(-Inf, -1, -0.5, -0.1, 0, 0.1, 0.5, 1, Inf),
  est.break.label = c("<-1", "[-1,-0.5)", "[-0.5,-0.1)", "[-0.1,0)", "[0,0.1)",
    "[0.1,0.5)", "[0.5,1)", ">=1"),
  neg.palette = "PuBu",
  pos.palette = "YlOrRd",
  p.sig.heat = "no",
  p.break = c(0, 1e-04, 0.05, 1),
  p.break.label = c("**", "*", ""),
  p.pool.break = c(0, 0.05, 1),
  p.pool.break.label = c("[0,0.05)", "[0.05,1]"),
  padjust.pool.break = c(0, 0.1, 1),
  padjust.pool.break.label = c("[0,0.1)", "[0.1,1]"),
  forest.est.shape = c("17", "16"),
  forest.est.col = c("red", "black"),
  forest.col = "by.pvalue",
  leg.key.size = 1,
  leg.text.size = 8,
  heat.text.x.size = 8,
  heat.text.x.angle = 0,
  forest.axis.text.y = 8,
  forest.axis.text.x = 8,
  heat.forest.width.ratio = c(1, 1),
  point.ratio = c(3, 1),
  line.ratio = c(2, 1)
)

Arguments

metadat

output data from metatab.show.

sumtype

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

level

"main" for main level such as phylum or "sub" for higher level such as species. Default is "main".

p

name of variable for p-values

p.adjust

name of variable for multiple testing adjusted p-values

phyla.col

type of color for main level (phylum). Options are "rainbow" (default) or "select".

phyla.select

selected phyla for selected colors (only when phyla.col="select"). Default are c("actinobacteria","bacteroidetes","cyanobacteria","firmicutes","fusobacteria","proteobacteria","verrucomicrobia",".thermi.").

col.select

selected colors for selected phyla (only when phyla.col="select"). Corresponding default are c("#dd1c77","#31a354","#91003f","#d95f0e","#636363","#2ef0e7","#862ef0","#000").

est.break

breaks for estimates to generate color categories on heatmap. Default are c(-Inf, -1,-0.5,-0.1,0,0.1,0.5,1, Inf). For pathway, recommended breaks are c(-Inf, -0.5,-0.1,-0.05,0,0.05,0.1,0.5, Inf).

est.break.label

labels for corresponding color categories on heatmap generated by est.break. Default corresponding to default est.break are c("<-1","[-1,-0.5)","[-0.5,-0.1)","[-0.1,0)", "[0,0.1)", "[01,0.5)", "[0.5,1)", ">=1"). For pathway, corresponding recommended labels are c("<-0.5)", "[-0.5,-0.1)","[-0.1,-0.05)","[-0.05,0)","[0,0.05)","[0.05,0.1)", "[0.1,0.5)", ">=0.5").

neg.palette

color palette for negative estimate values. Default is "PuBu". Use display.brewer.all() of RColorBrewer package for other options.

pos.palette

color palette for positive estimate values. Default is "YlOrRd". Use display.brewer.all() of RColorBrewer package for other options.

p.sig.heat

whether or not show significant p values on heatmap. Default is "yes".

p.break

breaks for significant levels of p values. Default is c(0, 0.0001,0.05, 1).

p.break.label

labels to be showed on heatmap for different levels of p-values from p.break. Default is c("**", "*","") for p breaks at c(0, 0.0001,0.05, 1).

p.pool.break

breaks for pooled p-values to be distinguished in forest plot. Default are c(0,0.05,1).

p.pool.break.label

labels for pooled p-value breaks. Corresponding default are c("[0,0.05)","[0.05,1]").

padjust.pool.break

breaks for multiple testing adjusted p-values to be distinguished in forest plot. Default are c(0,0.1,1).

padjust.pool.break.label

labels for multiple testing adjusted p-value breaks. Corresponding default are c("[0,0.1)","[0.1,1]").

forest.est.shape

point shape of pooled estimates in forest plot. Default are c("17","16") for corresponding significant and non-significant pooled estimates.

forest.est.col

colors of point (pooled estimates) and 95 CI bars in forest plot. Default are c("red", "black") for significant and non-significant estimates.

forest.col

Color of forest plot (point estimates and 95 CI). Options are "by.pvalue" (distinguished by signficant vs. non-significant p-value) or "by.estimate" (color scaled similarly to heatmap color).

leg.key.size

legdend key size for heatmap.

leg.text.size

legend text size for heatmap.

heat.text.x.size

heatmap x label text size.

heat.text.x.angle

heatmap x label text angle.

forest.axis.text.y

forest plot y label text size.

forest.axis.text.x

forest plot x label text size.

heat.forest.width.ratio

ratio of width between heatmap and forest plot to be used in grid.arrange. Dedault is c(1,1).

point.ratio

ratio of point size between significant pooled estimate and non-significant pooled estimate. Default is c(3,1).

line.ratio

ratio of error bar line size between significant pooled estimate and non-significant pooled estimate. Default is=c(2,1).

Value

combined heatmap forest plot.

Examples

# 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))