Plot the distributions of the normalized data as boxplots

Plot the distributions of the normalized data as boxplots

Usage

plot_boxplots(
  se,
  ain = NULL,
  color_by = NULL,
  label_by = NULL,
  facet_norm = TRUE,
  ncol = 3
)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomics data set

ain

Vector of strings which assay should be used as input (default NULL). If NULL then all normalization of the se object are plotted next to each other.

color_by

String specifying the column to color the samples (If NULL, the condition column of the SummarizedExperiment object is used. If "No", no color bar added.)

label_by

String specifying the column to label the samples (If NULL, the labels column of the SummarizedExperiment object is used. If "No", no labeling of samples done.)

facet_norm

Boolean specifying whether to facet by normalization methods (default TRUE). If FALSE, list of plots of the different normalized data is returned.

ncol

Number of columns in plot (for faceting)

Value

if facet_norm = TRUE, ggplot object, else list of ggplot objects

Examples

data(tuberculosis_TMT_se)
plot_boxplots(tuberculosis_TMT_se, ain = NULL, color_by = NULL, label_by = NULL,
              facet_norm = TRUE, ncol = 3)
#> All assays of the SummarizedExperiment will be used.
#> Condition of SummarizedExperiment used!
#> Label of SummarizedExperiment used!
#> Warning: Removed 9793 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 9793 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

plot_boxplots(tuberculosis_TMT_se, ain = c("log2", "IRS_on_RobNorm"), color_by = "Pool",
              label_by = "Label", facet_norm = FALSE)
#> $log2
#> Warning: Removed 1945 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 1945 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

#> 
#> $IRS_on_RobNorm
#> Warning: Removed 1979 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 1979 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

#>