plot_normalization {DEP} | R Documentation |
plot_normalization
generates boxplots
of all conditions for input objects, e.g. before and after normalization.
plot_normalization(se, ...)
se |
SummarizedExperiment,
Data object, e.g. before normalization (output from |
... |
Additional SummarizedExperiment object(s),
E.g. data object after normalization
(output from |
Boxplots of all conditions
for input objects, e.g. before and after normalization
(generated by ggplot
).
Adding components and other plot adjustments can be easily done
using the ggplot2 syntax (i.e. using '+')
# 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 and normalize filt <- filter_missval(se, thr = 0) norm <- normalize_vsn(filt) # Plot normalization plot_normalization(se, filt, norm)