meta.niceplot: Nice meta-analysis plots.

In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects

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))

metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.