--- title: "NMP Code" author: "Sahil Mapkar" date: "2024-03-19" updated: "2025-04-29" --- ## General Instruction *"GA3 Workflow.zip" consists of phenotypic extraction files* *"Tutorial.zip" consists of txt. file explaining how to run both source data and user generated input data* *"NMP Source Data.zip" consists of folder with all raw data and scripts to run for graphing output* *Below is explaination of code to users* ## NMP Code for edit ``` >library(umap) >library(ggplot2) >library(factoextra) >library("writexl") ``` *Import functions for data and graphing* *(umap) = R studio package UMAP (Version 0.2.10.0) - for dimensional reduction* (*ggplot2) = R studio package ggplot2 (version 3.3. 4) - for plotting* *(factoextra) = R studio package factoextra (Version 1.0.7) - for clustering* *("writexl") = R studio package UMAP (Version 1.5.0) - for excel exporting* ``` >Reduced_file_name <-file name ``` *Imported file name on the right and reduce file name on left* ``` >Name_data <-reduced file name[ ,columns] ``` *On the right put reduced file name and in brackets leave space empty for rows and after comma choose columns from file that will be used as 4 parameters. On left name data.* ``` >Name_scale <-scale(Name_data) ``` *Scale the data set.* ``` >umap_result <-umap(Name_scale, n_neighbors= #, n_components = #) ``` *Apply dimension reduction. Neighbors \# is traditionally set to 20. Components \# sets dimensionality. Component of 1 determines scores.* ``` >df_con <-data.frame(umap_result[["layout"]]) ``` *Frame all the data created by the UMAP function into an exportable format.* ``` >x <-df_con[ ,1] >y <-df_con [ ,2] >x <-unlist(x) >y <-unlist(y)ggplot(df_con, aes(x=x, y=y))+ geom_point() ``` *Parse out data points then plot for raw UMAP.* ``` >km.res <-kmeans(T_scale, #, nstart = #) >fviz_cluster(km.res, df_con, frame = FALSE, geom = "point") NMP Code.docx ``` *Apply clustering. \# determines number of clusters. nStart \# is traditionally set to 5.* ``` >km <-unlist(km.res) >km.matrix <-as.matrix(km) >km.df <-data.frame(km.matrix) ``` *Frame clustering data into an exportable format.* ``` >write_xlsx(km.df, "C:Users/Desktop\ FILE_NAME.xlsx") >write_xlsx(df_con, "C:Users/Desktop\ FILE_NAME.xlsx") ``` *Export data into an exportable excel.*