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nthomasCUBE authored Feb 14, 2020
1 parent bfd6488 commit 36b028f
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Showing 3 changed files with 140 additions and 12 deletions.
148 changes: 138 additions & 10 deletions methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -46,10 +46,13 @@ calc_cmp_transcriptomics_traits=function(v){
tabPanel("Linear model",
isolate(selectInput("gene2", "Gene-1",choices=cn2)),
isolate(selectInput("phen6", "Phenotype-1",choices=cn)),
isolate(selectInput("phen62", "Phenotype-1 (fixed or random)",choices=c("fixed model","random model"))),
isolate(selectInput("opt1", "operator-1",choices=c("---","*","+"))),
isolate(selectInput("phen7", "Phenotype-2",choices=cn)),
isolate(selectInput("phen72", "Phenotype-2 (fixed or random)",choices=c("fixed model","random model"))),
isolate(selectInput("opt2", "operator-2",choices=c("---","*","+"))),
isolate(selectInput("phen8", "Phenotype-3",choices=cn)),
isolate(selectInput("phen82", "Phenotype-3 (fixed or random)",choices=c("fixed model","random model"))),
isolate(textAreaInput("phen5_area", "Result", "", height = "400px")),
isolate(actionButton("go_alpha5", "Go!"))
))
Expand Down Expand Up @@ -154,7 +157,7 @@ cmp_traits=function(v,my_trait1,my_trait2,my_trait3){
}
}

linear_model=function(v, phen6, phen7, phen8, opt1, opt2, gene2){
linear_model=function(v, phen6, phen7, phen8, opt1, opt2, gene2, phen62, phen72, phen82){

expr=v$transcriptomics
trait=v$trait
Expand Down Expand Up @@ -187,28 +190,153 @@ linear_model=function(v, phen6, phen7, phen8, opt1, opt2, gene2){

if(phen8=="---"){
if(opt1=="*"){
o1=summary(lm(df[,1]~df[,2]*df[,3]))["coefficients"][[1]][,4]

if(phen62=="fixed model" && phen72=="fixed model"){
o1=summary(lm(df[,1]~df[,2]*df[,3]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model"){
o1=summary(lm(df[,1]~df[,2]*1|df[,3]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]*df[,3]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model"){
o1=summary(lm(df[,1]~1|df[,2]*1|df[,3]))["coefficients"][[1]][,4]
}
}
if(opt1=="+"){
o1=summary(lm(df[,1]~df[,2]+df[,3]))["coefficients"][[1]][,4]

if(phen62=="fixed model" && phen72=="fixed model"){
o1=summary(lm(df[,1]~df[,2]+df[,3]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model"){
o1=summary(lm(df[,1]~df[,2]+1|df[,3]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]+df[,3]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model"){
o1=summary(lm(df[,1]~1|df[,2]+1|df[,3]))["coefficients"][[1]][,4]
}
}
}else{
if(opt1=="*" && opt2=="*"){
o1=summary(lm(df[,1]~df[,2]*df[,3]*df[,4]))["coefficients"][[1]][,4]

if(phen62=="fixed model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]*df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]*df[,3]*1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]*1|df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]*1|df[,3]*1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]*df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]*df[,3]*1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]*1|df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]*1|df[,3]*1|df[,4]))["coefficients"][[1]][,4]
}
}
if(opt1=="*" && opt2=="+"){
o1=summary(lm(df[,1]~df[,2]*df[,3]+df[,4]))["coefficients"][[1]][,4]
if(phen62=="fixed model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]*df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]*df[,3]+1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]*1|df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]*1|df[,3]+1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(1|df[,1]~df[,2]*df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(1|df[,1]~df[,2]*df[,3]+1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(1|df[,1]~1|df[,2]*df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(1|df[,1]~1|df[,2]*df[,3]+1|df[,4]))["coefficients"][[1]][,4]
}
}
if(opt1=="+" && opt2=="*"){
o1=summary(lm(df[,1]~df[,2]+df[,3]*df[,4]))["coefficients"][[1]][,4]
if(phen62=="fixed model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]+df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]+df[,3]*1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]+1|df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]+1|df[,3]*1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]+df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]+df[,3]*1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]+1|df[,3]*df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]+1|df[,3]*1|df[,4]))["coefficients"][[1]][,4]
}
}
if(opt1=="+" && opt2=="+"){
o1=summary(lm(df[,1]~df[,2]+df[,3]+df[,4]))["coefficients"][[1]][,4]
if(phen62=="fixed model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]+df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]+df[,3]+1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~df[,2]+1|df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="fixed model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~df[,2]+1|df[,3]+1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]+df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="fixed model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]+df[,3]+1|df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="fixed model"){
o1=summary(lm(df[,1]~1|df[,2]+1|df[,3]+df[,4]))["coefficients"][[1]][,4]

}else if(phen62=="random model" && phen72=="random model" && phen82=="random model"){
o1=summary(lm(df[,1]~1|df[,2]+1|df[,3]+1|df[,4]))["coefficients"][[1]][,4]
}
}
}

o1=summary(lm(df[,1]~df[,2]*df[,3]))["coefficients"][[1]][,4]
o2=rownames(summary(lm(df[,1]~df[,2]*df[,3]))["coefficients"][[1]])

print(summary(df))
o2=rownames(as.data.frame(o1))
print(o1)
print(o2)
print(length(o2))
if(length(o2)==4){
o2[2]=phen6
o2[3]=phen7
o2[4]=paste(phen6,phen7)
}

o12=c()
o12=c(o12,"contrast\tp-value\n")
Expand Down
2 changes: 1 addition & 1 deletion run_traitCorr.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# to run traitCorr and finally open the R Shiny instance of traitCorr
#

packages_necessary=c("d3heatmap","gplots","officer","VennDiagram","scales","shiny","shinyalert","shinyBS","shinyjs","shinythemes","xlsx")
packages_necessary=c("d3heatmap","gplots","officer","VennDiagram","scales","shiny","shinyalert","shinyBS","shinyjs","shinythemes","xlsx","plm")
for(x in 1:length(packages_necessary)){
print(packages_necessary[x])
library(packages_necessary[x],character.only=TRUE)
Expand Down
2 changes: 1 addition & 1 deletion server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ server <- function(input, output, session)
observeEvent(input$go_alpha5,{
source("methods.R")
output$plot=renderPlot({
res=linear_model(v,input$phen6,input$phen7,input$phen8,input$opt1,input$opt2,input$gene2)
res=linear_model(v,input$phen6,input$phen7,input$phen8,input$opt1,input$opt2,input$gene2,input$phen62,input$phen72,input$phen82)
updateTextAreaInput(session, "phen5_area", label = "", value = res)

})
Expand Down

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