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Plot a heatmap of proteins with missing values

plot_missval.Rd

plot_missval generates a heatmap of proteins with missing values to discover whether values are missing by random or not.

Usage

plot_missval(se, ...)

Arguments

se

SummarizedExperiment

...

Additional arguments for Heatmap function as depicted in Heatmap Data object with missing values.

Value

A heatmap indicating whether values are missing (0) or not (1) (generated by Heatmap).

Examples

# Load example
data(Silicosis_pg)
data <- Silicosis_pg
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Differential test
ecols <- grep("LFQ.", colnames(data_unique))
se <- make_se_parse(data_unique, ecols,mode = "delim")
filt <- filter_se(se, thr = 0, fraction = 0.4, filter_formula = ~ Reverse != "+" & Potential.contaminant!="+")
#> filter base on missing number is <= 0 in at least one condition.
#> filter base on missing number fraction < 0.4 in each row
#> filter base on giving formula 

# Plot missing values heatmap
plot_missval(filt)