inst/shiny/PathoStat/utils/old_ui_stuff.R

In PathoStat: PathoStat Statistical Microbiome Analysis Package

library(shiny)
library(shinyjs)
library(phyloseq)
library(plotly)
source(file.path("utils", "helpers.R"))



alpha.methods <- c("Shannon", "Simpson", "InvSimpson")
# Weigthed Unifrac, Bray-Curtis
beta.methods <- c("wUniFrac", "bray")

tax.name <- c('superkingdom', 'kingdom', 'phylum', 'class', 'order', 'family',
    'genus', 'species', 'no rank')
norm.methods <- c('EBayes coreOTU Normalization',
    'Quantile coreOTU Normalization', 'Library Size Scaling')
measure.type <- c('Final Guess', 'Final Best Hit', 'Final High Confidence Hit')
minbatch <- function(batch1){
    batch2 <- as.factor(batch1)
    batch3 <- split(batch1,batch2)
    return(min(unlist(lapply(1:length(batch3),
        function(x) length(batch3[[x]])))))
}

shinyInput <- getShinyInput()

pstat <- shinyInput$pstat
covariates <- colnames(sample_data(pstat))

# choose the covariates that has less than 8 levels
covariates.colorbar <- c()
for (i in 1:length(covariates)){
  num.levels <- length(unique(sample_data(pstat)[[covariates[i]]]))
  if (num.levels < 8){
    covariates.colorbar <- c(covariates.colorbar, covariates[i])
  }
}

# choose the covariates that has 2 levels
covariates.two.levels <- c()
for (i in 1:length(covariates)){
  num.levels <- length(unique(sample_data(pstat)[[covariates[i]]]))
  if (num.levels == 2){
    covariates.two.levels <- c(covariates.two.levels, covariates[i])
  }
}

is.categorical <- function(v) {
  if (class(v) == "integer" || class(v) == "numeric") {
    return(F)
  } else {
    return(T)
  }
}

# numeric cov
    sam_temp <- as.data.frame(pstat@sam_data)
    num_select <- lapply(covariates, function(x) is.categorical(unlist(sam_temp[,x])))
    num_covariates <- covariates[!unlist(num_select)]



maxbatchElems <- minbatch(c(pstat@sam_data[,1])[[1]])
maxcondElems <- minbatch(c(pstat@sam_data[,2])[[1]])
defaultDisp <- 30
defaultGenesDisp <- 10
maxGenes <- dim(pstat@otu_table)[1]




#sample name
sample.names.all <- colnames(pstat@otu_table@.Data)