plot_single: Plot values for a protein of interest

In squirrelandr/DEP: Differential Enrichment analysis of Proteomics data

Description

plot_single generates a barplot of a protein of interest.

Usage

plot_single(dep, proteins, type = c("contrast", "centered"), plot = TRUE)

Arguments

dep	SummarizedExperiment, Data object for which differentially enriched proteins are annotated (output from test_diff() and add_rejections()).
proteins	Character, The name(s) of the protein(s) to plot.
type	'contrast' or 'centered', The type of data scaling used for plotting. Either the fold change ('contrast') or the centered log2-intensity ('centered').
plot	Logical(1), If TRUE (default) the barplot is produced. Otherwise (if FALSE), the summaries which the barplot is based on are returned.

Value

A barplot (generated by ggplot).

Examples

# Load example
data <- UbiLength
data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Make SummarizedExperiment
columns <- grep("LFQ.", colnames(data_unique))
exp_design <- UbiLength_ExpDesign
se <- make_se(data_unique, columns, exp_design)

# Filter, normalize and impute missing values
filt <- filter_missval(se, thr = 0)
norm <- normalize_vsn(filt)
imputed <- impute(norm, fun = "MinProb", q = 0.01)

# Test for differentially expressed proteins
diff <- test_diff(imputed, "control", "Ctrl")
dep <- add_rejections(diff, alpha = 0.05, lfc = 1)

# Plot single proteins
plot_single(dep, 'USP15')
plot_single(dep, 'USP15', 'centered')
plot_single(dep, c('USP15', 'CUL1'))
plot_single(dep, c('USP15', 'CUL1'), plot = FALSE)

squirrelandr/DEP documentation built on May 7, 2019, 9:31 a.m.