plotDECOProfile: Feature profile from DECO analysis

In fjcamlab/deco: Decomposing Heterogeneous Cohorts using Omic Data Profiling

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. <[e-mail]>

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)])

fjcamlab/deco documentation built on Aug. 18, 2024, 4:28 a.m.