Functional analysis: MCA - add distance method

[ChristinaSchmidt1]

I will add clustering based on distance and double check the clustering we have now between the two conditions (and potentially update it for more functionality).

[ChristinaSchmidt1]

Add to MCA_CoRe:

• rename Consumed by Cond1 and Released by Cond2 or vice versa into Consumed/Released to fit with terminology I use.
• Write a helper function to import the clustering overview DFs
• Include labelling function here, that based on sign (release./consumed) and Log2FC labels columns in the way we need it if user has not started from our DMA output

Add to MCA_2Cond:

• rename Cond1 and Cond2 to use the name the user has given for this column

Add MCA_Distance:

• Give the parameter to either provide distance value cutoff or to do it based on data distribution?
• cluster metabolites in buckets based on their distance of change --> the higest distance of change would lead to great lollipop graphs

Generally:

• Put results into one excel file with multiple sheets
• enable user to add vector to rename clusters
• Make extra function to run ORA on each individual cluster and plot results

[ChristinaSchmidt1]

#' MCA_Distance
#'
#' This script allows you to perform metabolite clustering analysis and computes clusters of metabolites based on regulatory rules between two conditions.
#'
#' @param Cond1_File DF for your data (results from e.g. DMA) containing metabolites in rows with corresponding Log2FC and stat (p-value, p.adjusted) value columns.
#' @param Cond2_File DF for your data (results from e.g. DMA) containing metabolites in rows with corresponding Log2FC and stat (p-value, p.adjusted) value columns.
#' @param MetaboliteID Column name of Column including the Metabolite identifiers. This MUST BE THE SAME in each of your Input files.
#' @param Cond1ValueCol Column name of Log2FC in Cond1File
#' @param Cond1PadjCol Column name of adjusted p-value in Cond1File. Can also be you p-value column if you want to use this instead.
#' @param Cond2ValueCol  Column name of Log2FC in Cond2File
#' @param Cond2PadjCol Column name of adjusted p-value in Cond2File. Can also be you p-value column if you want to use this instead.
#' @param Cond1_padj_cutoff  \emph{Optional: } adjusted p-value cutoff for Cond1File. \strong{Default=0.05}
#' @param Cond2_padj_cutoff \emph{Optional: } adjusted p-value cutoff for Cond2File. \strong{Default=0.05}
#' @param backgroundMethod \emph{Optional: } Background method C1|C2, C1&C2, C2, C1 or * \strong{Default="C1&C2"}
#' @param outputFileName \emph{Optional: } Output filename \strong{Default=SiRCle_RCM.csv}
#' @return MCA an instance of the MetaProViz package
#' @export
#'

##################################################
### ### ### Metabolite Clustering Analysis ### ### ###
##################################################

#MCA_Distance <- function(Cond1_File, Cond2_File, MetaboliteID= "Metabolite", Cond1ValueCol="Log2FC",Cond1PadjCol="p.adj", Cond2ValueCol="Log2FC", Cond2PadjCol="p.adj",Cond1_padj_cutoff= 0.05, Cond2_padj_cutoff = 0.05, backgroundMethod="C1&C2", OutputFileName = "MCA_Distance_")