R/multiple_contrast_test.R

In MoisesExpositoAlonso/moiR: A set of R functions for an easy life and analyses

# #' Quick plot + contrast hypothesis test to compare two populations
# #'
# #' @param numeric1 a numeric vector of group 1
# #' @param numeric2 a numeric vector of group 2
# #' @param method string, either t.student (parametric) or wilcox.test (nonparametric)
# #' @param title string with the name of the plot
# #' @param wantpoints Logical FALSE/TRUE to determine whether points will be overplotted
# #' @param wantviolin Logical FALSE/TRUE to determine whether you want a violine plot in the background
# #' @param The colors of the two groups. Default c("darkorchid4","aquamarine4")
# #'
# #' @return Prints a plot with the given test p-value. If title is provided, it prints into a pdf.
# #'
# #' @examples
# #' group1=rnorm(n = 100,mean = 1,sd = 1)
# #' group1=rnorm(n = 100,mean = 2,sd = 1)
# #' thetimenow<-contrast_test(group1,group2)
# #'
# #' @export
# #'


# g1=rnorm(n = 100,mean = 1,sd = 1)
# g2=rnorm(n = 100,mean = 2,sd = 1)
# g3=rnorm(100,3,1)
# data<-data.frame(numbers=c(g1,g2,g3),factors=c( rep(1,100),rep(2,100),rep(3,100))  )
# thetimenow<-contrast_test(group1,group2,group3)

# contrast_test<-function(numbers,factors,method ="t.test",title=NULL,wantpoints=FALSE,wantviolin=TRUE,colorpair=c("darkorchid4","aquamarine4")){

# data=data.frame(numbers,factors)

# numeric1name=deparse(substitute(numeric1))
# numeric2name=deparse(substitute(numeric2))

# # decide whith test
# if(method =="t.test"){  mytest<-t.test(numeric1,numeric2) }
# else if (method=="wilcox.test") { mytest<-wilcox.test(numeric1,numeric2)  }
# else{print("need to provide appropriate test: t.test or wilcox.test")}
# p<-format(mytest$p.value,digits=3)

# #print test
# print(mytest)

# # go for plot
# if(!is.null(title)){
# write.pdf(paste("contrast_plot",title,numeric1name,numeric2name,sep="_"))
# }

#       # type boxplot
#       if(wantviolin ==F ){
#       boxplot(numeric1,numeric2,col=transparent(colorpair),borders="white", names=c(numeric1name,numeric2name))
#       mtext(paste(method,"p = ",p ),side = 1)
#       # text(x=1.5,y=max(c(numeric1,numeric2)),labels = format(p,digits=4) )
#         if(wantpoints==T ){
#         points(y= numeric1, pch=19,col=transparent("black",alpha = 0.2) , x=jitter(rep(1,length(numeric1)),factor = 2))
#         points(y= numeric2, pch=19,col=transparent("black",alpha = 0.2) , x=jitter(rep(2,length(numeric2)),factor=2))
#         }}

#       # type violin
#       else if(wantviolin==T){
#       library(ggplot2)
#       library(cowplot)
#       numeric1data<-data.frame(variable=numeric1name,value=numeric1)
#       numeric2data<-data.frame(variable=numeric2name,value=numeric2)
#       toplot_melt<-rbind(numeric1data,numeric2data)

#       p<-ggplot(data=toplot_melt)+geom_violin(trim=FALSE,aes(x = variable,y=value,fill=variable),alpha=0.2)+ theme_cowplot()+xlab("")+ylab("")+
#        scale_fill_manual(values =colorpair,guide=F )+geom_boxplot(aes(x = variable,y=value ),color=colorpair,width=0.2)+ggtitle(paste(method,"p = ",p ))
#         if(wantpoints==T ){
#         p<-p + geom_point(aes(x = variable,y=value,color=variable))+scale_color_manual(values=transparent(colorpair))
#         print(p)
#         }else{print(p)}
#       }

# # print if required
# if(!is.null(title)){  dev.off()  }

# }