MS data from MaxQuant.

knitr::opts_chunk$set(echo = FALSE, warning = F)

Experiment design

if (!is.null(params$experimentDesign)) {

     kableExtra::kbl(params$experimentDesign, align = 'c') 
}

if (!is.null(params$contaminants)) {

    print(params$contaminants)
}

if (!is.null(params$missingValues)) {

    print(params$missingValues)
}

if (!is.null(params$normalization)) {

    print(params$normalization)
}

if (!is.null(params$imputation)) {

    print(params$imputation)
}

if (!is.null(params$scatter)) {

    print(params$scatter)        
}

if (!is.null(params$correlation)) {

    MQanalyser::plot_correlationly(params$correlation, interactive = F) 

}

if (!is.null(params$PCA)) {

    print(params$PCA)            
}

if (!is.null(params$heatMap)) {

    if (params$heatMapTopContributors == TRUE) {

        MQanalyser::plot_heatmaply(dep = params$heatMap$dep,
                       intensity_type = params$heatMap$IntensityType,
                       top_contributors = params$heatMap$topContributors,
                       interactive = FALSE)
    }else{
        print(params$heatMap)
    }
}

if (!is.null(params$heatmap2)) {

    print(params$heatmap2)            
}

if (!is.null(params$volcano)) {

    print(params$volcano)            
}

if (!is.null(params$profile)) {

    print(params$profile)            
}

if (!is.null(params$geneOntology)) {

    print(params$geneOntology)            
}

if (!is.null(params$GSEAenrichment)) {

    print(params$GSEAenrichment)            
}

if (!is.null(params$networkEnrichment)) {

    print(params$networkEnrichment)            
}

if (!is.null(params$diseaseaseEnrinchment)) {

    print(params$diseaseaseEnrinchment)            
}

if (!is.null(params$diseaseaseGSEA)) {

    print(params$diseaseaseGSEA)            
}

if (!is.null(params$diseaseaseHeatmap)) {

    print(params$diseaseaseHeatmap)            
}

if (!is.null(params$diseaseaseDensity)) {

    print(params$diseaseaseDensity)            
}

if (!is.null(params$diseaseaseAssociation)) {

    print(params$diseaseaseAssociation)            
}

if (!is.null(params$diseaseaseCircus)) {

    print(params$diseaseaseCircus)            
}

if (!is.null(params$diseaseaseNetwork)) {

    print(params$diseaseaseNetwork)            
}

if (!is.null(params$diseaseaseMap)) {

    print(params$diseaseaseMap)            
}

if (!is.null(params$pathway)) {

    print(params$pathway)            
}

if (!is.null(params$interactions)) {

    string_db <- STRINGdb$new(version = "11.5", species=9606,
                               score_threshold = 200, input_directory="")

    print(string_db$plot_network(params$interactions))            
}