plot_design: Plot Univariate Effects for genes associated with a Gene...
In GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

Description Usage Arguments Value Author(s) See Also Examples

Successively plots univariate effects of one or more factors, typically for a designed experiment as analyzed by aov().

1
2
3

plot_design(
    go_id, result, eSet, subset=NULL,
    factors=colnames(pData(eSet)), main="", main.Lsplit=NULL, ...)

`go_id`	A Gene Ontology (GO) identifier represented by at least one gene in the dataset.
`result`	The output of `GO_analyse()` or a subset of it obtained from `subset_scores()`.
`eSet`	`ExpressionSet` of the `Biobase` package including a gene-by-sample expression matrix in the `AssayData` slot, and a phenotypic information data-frame in the `phenodata` slot. In the expression matrix, row names are Ensembl gene identifiers or probeset identifiers, and column names are sample identifiers. In the phentypic data-frame, row names are sample idenfifiers, column names are grouping factors and phenotypic traits usable for the one-way ANOVA.
`subset`	A named list to subset `eSet`. Names must be column names existing in colnames(pData(eSet)). Values must be vectors of values existing in the corresponding column of pData(eSet).
`factors`	A set of column names from `phenodata`. Each of these values will be represented on the X-axis to investigate its effect on the average expression of a given genes for each level of that factor.
`main`	Changes the main title of the plots.
`main.Lsplit`	Number of characters after which a new-line character will be inserted in the main title. If this would occur within a word, the new-line character will be inserted before this word. Default is NULL, leaving the title on a single line.
`...`	Additional arguments which will be passed on to the `plot.design`() function.

The output of the plot.design() function.

Kevin Rue-Albrecht

Method plot.design.

# load the sample output data
data(AlvMac_results)

# Univariate plot
plot_design(go_id="GO:0034142", eSet=AlvMac, result=AlvMac_results)

Loading required package: grid
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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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")'.