Plot a heatmap of the sample intensities with optional column annotations for a selection of normalization methods

Plot a heatmap of the sample intensities with optional column annotations for a selection of normalization methods

Usage

plot_heatmap(
  se,
  ain = NULL,
  color_by = c("Group", "Pool"),
  label_by = NULL,
  only_refs = FALSE
)

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

Vector of strings specifying the columns to color the samples (If NULL, the condition column of the SummarizedExperiment object is used. If "No", no color bars added.)

label_by

String specifying the column in the metadata used to label the samples for the UpSet plot

only_refs

Logical, if TRUE, only reference samples (ComRef) are included in the plot

Value

list of ggplot objects

Examples

data(tuberculosis_TMT_se)
plot_heatmap(tuberculosis_TMT_se, ain = c("log2"), color_by = NULL,
             label_by = NULL, only_refs = FALSE)
#> Condition of SummarizedExperiment used!
#> Label of SummarizedExperiment used!
#> $log2

#>