code for figures/Figure3_aminoglycosideassociations_4sp.R

In pmtran5884/Glycancc: Community Clustering of Anti-Carbohydrate Antibody data

#Aminoglycaside T1D associations
#Date: March 9, 2022
#Author: Paul Tran
#Updated: March 9, 2022
rm(list = ls())

########## HELPER FUNCTIONS #####################
source("C:/Users/spurohit/Box/Sharad_DataShare/Papers/Students/T1D glycan array data/aca_rep_t1d/scripts/helper_functions_v2.R")

########## Libraries #############
# BiocManager::install("PCAtools")
# devtools::install_github("jokergoo/ComplexHeatmap")

library(pacman)
library(PCAtools)
library(ComplexHeatmap)
p_load("xlsx")
p_load("umap")
p_load("igraph")
p_load("ggplot2")
p_load("alluvial")
p_load("Hmisc")
p_load("fastDummies")
p_load("dplyr")
p_load("gmodels")
p_load("gtsummary")
p_load("dendextend")
p_load("circlize")
p_load("Ryacas")
p_load("PCAtools")
p_load("BiocManager")
p_load("pROC")
p_load("fmsb")
p_load("glmnet")

####### set seed ##########
set.seed(123)

######## LOAD AND cLEAN DATA ################
daisy<-load_and_clean_DAISY_data(dataloc="c:/Users/spurohit/Box/Sharad_DataShare/Papers/Students/T1D glycan array data/aca_rep_t1d/raw data/1b_NGCBgMFI_Pheno data for_IgG_DAISY.csv",
                                 phenoloc="c:/Users/spurohit/Box/Sharad_DataShare/Papers/Students/T1D glycan array data/aca_rep_t1d/raw data/1_DAISY112_phenotype data.xls",
                                 removeoutliers = F, 
                                 backgroundThesholdval = 1,
                                 log2=T)

glycan_classes<-load_glycan_classes("c:/Users/spurohit/Box/Sharad_DataShare/Papers/Students/T1D glycan array data/aca_rep_t1d/raw data/glycan_classes.csv")

univariate_radar_chart(daisy=daisy,gly_class="Aminoglycoside antibiotics")