correlations.Rmd

---
title: "Correlations"
author: "Xingyao Chen"
date: "6/21/2017"
output:
  html_document: default
  pdf_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(cache = TRUE)
#install.packages('GGally')
#install.paackages('ggplot2)
#install.packages("qtlcharts",  repos = 'http://cran.rstudio.com/')
library(GGally)
library(qtlcharts)
library(ggplot2)
my_fn <- function(data, mapping, ...){
  p <- ggplot(data = data, mapping = mapping) + 
    geom_point(size=0.5) + 
    geom_smooth(method=lm, fill="blue4", color="blue1", ...)
  return(p)
}
```

```{r}
mydat_small=read.csv('pollinator_visitation_fullData.csv')[,-1]

mydat_small$Experiment.Week=as.factor(mydat_small$Experiment.Week)
mydat_small$Plant.Number=as.factor(mydat_small$Plant.Number)
mydat_small$Pair=as.factor(mydat_small$Pair)

mydat_small_log=read.csv('pollinator_visitation_fullData_logTrans.csv')[,-1]

mydat_small_log$Experiment.Week=as.factor(mydat_small_log$Experiment.Week)
mydat_small_log$Plant.Number=as.factor(mydat_small_log$Plant.Number)
mydat_small_log$Pair=as.factor(mydat_small_log$Pair)

```


##Make a pairwise correlation plot for the untransformed data
```{r, warning=F}
boo=c()
for (i in 1:ncol(mydat_small)){
  boo[i]=is.numeric(mydat_small[,i])
}
ggpairs(mydat_small[,boo][,-c(9:10,12:13)], lower=list(continuous=my_fn))
```


#This is a more complete correlation heatmap, and it's interactive! (Only on html verson of Rmd)
```{r}
p1=iplotCorr(mydat_small[,boo],mydat_small$visits, reorder=TRUE,
          chartOpts=list(cortitle="Correlation Heatmap, Untransformed",
                         scattitle="Scatterplot | Visits",
                         scatcolors=c("red","lightblue")
          ))
p1
```



##Make a pairwise correlation plot for the log transformed data
```{r, warning=F}
ggpairs(mydat_small_log[,boo][,-c(9:10,12:13)], lower=list(continuous=my_fn))
```


#Now the interactive heatmap (Only on html verson of Rmd)

```{r, corheat}
p2=iplotCorr(mydat_small_log[,boo],mydat_small_log$visits, reorder=TRUE,
          chartOpts=list(cortitle="Correlation Heatmap, Log10 Transformed",
                         scattitle="Scatterplot | Visits",
                         scatcolors=c("red","lightblue")
          ))
p2
```