plotExwas-methods: Function to draw a plot of the pvalues stored in an 'ExWAS'...

In rexposome: Exposome exploration and outcome data analysis

Description

This function draws a sort of manhattan plots using the p-value of the association of the exposures with phenotypes of an ExWAS object.

Usage

plotExwas(
  object,
  ...,
  subtitles,
  color,
  exp.order,
  labels,
  show.effective = TRUE
)

Arguments

object	An ExWAS object which p-values will be plotted.
...	Other objects of class ExWAS.
subtitles	(optional) Characters used as "substitle" when more than one ExWAS is given.
color	(optional) Character vector of HTML colors, labeled with family's names. Used to colore the exposures.
exp.order	(optional) Character vector of exposures used to order and subset the plot.
labels	(optional) Character vector with the labels for each exposure. It must be labeled vector.
show.effective	(default TRUE) If set to FALSE, line showing effective test threshold is not shown.

Value

An object of class ggplot.

See Also

exwas as a constructor for ExWAS objects, extract to obtain a table with the result of the ExWAS

Examples

data(exposome)
w1 <- exwas(expo[1:5, ], asthma~1, family = "binomial")
plotExwas(w1)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Registered S3 method overwritten by 'pryr':
  method      from
  print.bytes Rcpp

Attaching package: ‘rexposome’

The following object is masked from ‘package:BiocGenerics’:

    plotPCA

Warning message:
In exwas(expo[1:5, ], asthma ~ 1, family = "binomial") :
  Data from 'asthma~lddt_lip+1' was reduced from 1200 to 1185

rexposome documentation built on March 13, 2021, 2:01 a.m.