plotDECOProfile {deco} | R Documentation

## Feature profile from DECO analysis

### Description

Plot feature profile(s) in a separate PDF from decoReport R function.

### Usage

    plotDECOProfile(deco, id, data, pdf.file = NA, plot.h = FALSE,
                          info.sample = NA, print.annot = FALSE,
                          cex.legend = 1.1, cex.names = 1, cex.samples = 1)

### Arguments

`deco` | a "deco" R object generated by 'decoNSCA' R function.
`id` | character vector indicating what original IDs from input data should be highlighted and plot in 'Profile' section. If all IDs found have to be plot, input all corresponding IDs here.
`data` | input matrix of normalized data with 'f' features (rows) by 's' samples (columns).
`pdf.file` | path or name of pdf where report should be generated.
`plot.h` | logical indicating if points corresponding to 'h' relative values should be plotted.
`info.sample` | a factor or data.frame with relevant information of samples to be plot on 'Heatmap'.
`print.annot` | logical indicating if annotation (gene SYMBOL) should be printed instead original IDs. This option needs previous annotation within 'decoRDA' function or late annotation binding information to @featureTable slot of 'deco' R object.
`cex.legend` | numerical value giving the amount of magnification of legend.
`cex.names` | numerical value giving the amount of magnification to gene names or sample names.
`cex.samples` | numerical value giving the amount of magnification of sample related information, i.e. sample points in 'Profile' plots.

### Value

Returns a new PDF.

### Author(s)

Francisco Jose Campos Laborie. <fjcamlab@usal.es>

### See Also

`decoNSCA`, `voom`

### Examples

    #### Further information in DECO vignette(s).
    ## Run after decoRDA and decoNSCA steps on 'ALCLdata'
    data(ALCLdata)
    ALCL

    ### ERBB4 gene profile
    # plotDECOProfile(deco = deco.results.ma, id = "ENSG00000178568",
    #                 data = assay(ALCL), cex.samples = 2,
    #                 pdf.file = "ERBB4_profile_ALCL.pdf",
    #                 info.sample = as.data.frame(colData(ALCL))[,c(9,8,10)])

[Package deco version 1.0.0 Index]