plot_single {DEP} | R Documentation |
plot_single
generates a barplot of a protein of interest.
plot_single(dep, proteins, type = c("contrast", "centered"), plot = TRUE)
dep |
SummarizedExperiment,
Data object for which differentially enriched proteins are annotated
(output from |
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 |
A barplot (generated by ggplot
).
# 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)