Barplot of coverage of DE markers per normalization method in any comparison. (If you want to have a look at a specific comparison, just subset the de_res data table before plotting.)

Barplot of coverage of DE markers per normalization method in any comparison. (If you want to have a look at a specific comparison, just subset the de_res data table before plotting.)

Usage

plot_coverage_DE_markers(se, de_res, ain, markers, id_column = "Protein.IDs")

Arguments

se

SummarizedExperiment containing all necessary information of the proteomics data set

de_res

data table resulting of run_DE

ain

Vector of strings of normalization methods to visualize (must be valid normalization methods saved in de_res)

markers

vector of the IDs of the markers to plot

id_column

String specifying the column of the rowData of the SummarizedExperiment object which includes the IDs of the markers

Value

ggplot object

Examples

data(tuberculosis_TMT_se)
data(tuberculosis_TMT_de_res)
plot_coverage_DE_markers(tuberculosis_TMT_se, tuberculosis_TMT_de_res,
                          ain = NULL, markers = c("Q7Z7F0", "Q13790"),
                          id_column = "Protein.IDs")
#> All assays of the SummarizedExperiment will be used.
#> All comparisons of de_res will be visualized.
#> Warning: raw: not valid normalization methods. Only valid normalization methods will be visualized.