saezlab / MetaProViz

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
https://saezlab.github.io/MetaProViz/
GNU General Public License v3.0
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Functional analysis: MCA - Add kmeans clustering to MCA #26

Open dprymidis opened 1 year ago

ChristinaSchmidt1 commented 1 year ago

I have worked on the MCA file and created/updated) already the two functions for doing MCA on 2 conditions (MCA_2Cond) or with CoRe data (MCA_CoRe). Please use the same parameter names where applicable for the kmeans function. I also added a parameter so the user can pass their column name in case they have not the same names as we have (default are the names of the DMA output).

I have created a placeholder for you to move the kmeans at the bottom of the R file.

#' MCA_KMeans
#'
#' This script allows you to perform kmeans clustering to compute clusters of metabolites.
#'
#' @param 
#' @param outputFileName \emph{Optional: } Output filename \strong{Default=SiRCle_RCM.csv}
#' @return MCA an instance of the MetaProViz package
#' @export
#'

###############################################################
### ### ### Metabolite Clustering Analysis: K-means ### ### ###
###############################################################

MCA_KMeans <- function()
ChristinaSchmidt1 commented 1 year ago

Also, please name the new column with the reuslts RG1_kmeans

ChristinaSchmidt1 commented 1 year ago

As we discussed in yesterdays meeting, lets talk about the parameter syntax in a dedicated meeting to decide if we can make it similar to the RCM functions or if we should have a similar syntax to heatmap.