plotDECOProfile: Feature profile from DECO analysis
In deco: Decomposing Heterogeneous Cohorts using Omic Data Profiling

Description Usage Arguments Value Author(s) See Also Examples

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

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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)

`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.

Returns a new PDF.

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

decoNSCA, voom

#### 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)])