meanSdPlot {DEP} | R Documentation |
meanSdPlot
generates a hexagonal heatmap
of the row standard deviations versus row means
from SummarizedExperiment objects.
See meanSdPlot
.
meanSdPlot(x, ranks = TRUE, xlab = ifelse(ranks, "rank(mean)", "mean"), ylab = "sd", pch, plot = TRUE, bins = 50, ...)
x |
SummarizedExperiment, Data object. |
ranks |
Logical, Whether or not to plot the row means on the rank scale. |
xlab |
Character, x-axis label. |
ylab |
Character, y-axis label. |
pch |
Ignored - exists for backward compatibility. |
plot |
Logical, Whether or not to produce the plot. |
bins |
Numeric vector, Data object before normalization. |
... |
Other arguments,
Passed to |
A scatter plot of row standard deviations
versus row means(generated by stat_binhex
)
# 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 meanSdPlot meanSdPlot(norm)