plot_all: Visualize the results in different types of plots
In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

Description Usage Arguments Value Examples

plot_all visualizes the results of the differential protein expression analysis in different types of plots. These are (1) volcano plots, (2) heatmaps, (3) single protein plots, (4) frequency plots and/or (5) comparison plots.

1 2	plot_all(dep, plots = c("volcano", "heatmap", "single", "freq", "comparison"))

`dep`	SummarizedExperiment, Data object which has been generated by `analyze_dep` or the combination of `test_diff` and `add_rejections`.
`plots`	"volcano", "heatmap", "single", "freq" and/or "comparison",

Pdfs containg the desired plots.

# Load datasets
data <- UbiLength
exp_design <- UbiLength_ExpDesign

# Import and process data
se <- import_MaxQuant(data, exp_design)
processed <- process(se)

# Differential protein expression analysis
dep <- analyze_dep(processed, "control", "Ctrl")

## Not run: 
# Plot all plots
plot_all(dep)

## End(Not run)