index.Rmd

---
title: "Love Triangle: An Activity-Phylogeny-Function Relationship"
author: "Constantinos Xenophontos"
date: "February 19, 2019"
output: html_document
---

<style>
.main-container {
  max-width: 1800px;
  margin-left: 500px;
  margin-right: auto;
}
</style>

```{r, setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r, echo=FALSE, message=FALSE, warning=FALSE}
##############################################################

library(openxlsx)
library(ggplot2)
library(plotly)
library(gg3D)
library(scatterplot3d)
library(RColorBrewer)

##############################################################

APF3D <- read.xlsx("C:/Users/Constantinos/Desktop/Mixed Cultures Experiment - 2018/Assay-25_Fluorescence Assays Rates/Clusters/Activity-Dissimilarity matrix.xlsx")

colnames(APF3D)[colnames(APF3D)=="Activity.change"] <- "Activity_change"
colnames(APF3D)[colnames(APF3D)=="Phyl..Distance"] <- "Phylogenetic_Diversity"
colnames(APF3D)[colnames(APF3D)=="Fun..Distance"] <- "Functional_Diversity"

APF3D.log <- APF3D

APF3D.log$Activity_change <- log10(APF3D$Activity_change+101)

##############################################################
```

```{r, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE}
##############################################################

## Assay-25 Communities data
comms <- read.xlsx("C:/Users/Constantinos/Desktop/Mixed Cultures Experiment - 2018/Assay-25_Fluorescence Assays Rates/Clusters/PCA/comms.xlsx", sheet = "rates", check.names = FALSE)

comms.100 <- read.xlsx("C:/Users/Constantinos/Desktop/Mixed Cultures Experiment - 2018/Assay-25_Fluorescence Assays Rates/Clusters/PCA/comms.xlsx", sheet = "% change", check.names = FALSE)

# Prepare PCA dataframe
# comms.pca <- comms[c(3:13)]
# comms.pca.z <- scale(comms.pca)
# comms.pca.log <- log10(comms.pca+1)

comms.pca.100 <- comms.100[c(3:13)]
comms.pca.100.z <- scale(comms.pca.100)
comms.pca.100.log <- as.data.frame(log10(comms.pca.100+101))

comms.pca.100[is.na(comms.pca.100)] <- 0
comms.pca.100.z[is.na(comms.pca.100.z)] <- 0
comms.pca.100.log[is.na(comms.pca.100.log)] <- 0
##############################################################
```

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### Community proportional activity changes (Fisher's z transformed) PCA

```{r, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE}
##############################################################

## 3D PCA of Fisher's z -scale transformed communities

pca7 <- prcomp(comms.pca.100.z,
               center = TRUE)

# Scores
scores <- pca7$x
x <- scores[,1]
y <- scores[,2]
z <- scores[,3]

# 3D plot
attach(comms)
plot_ly(x = x, y = y, z = z,
            type="scatter3d",
            mode="markers",
            color = ~Group,
            colors = c("#F8766D","#7CAE00", "#00BFC4", "#C77CFF"),
            marker = list(size = 10,
                          line = list(color = "black",
                                      width = 1))) %>%
  layout(scene = list(xaxis = list(title = "PC1 (50.23%)"),
                      yaxis = list(title = "PC2 (16.56%)"),
                      zaxis = list(title = "PC3 (10.01%")),
         margin = list(r = 0,
                       t = 0,
                       b = 0,
                       l = 0,
                       pad = 0),
         legend = list(x = 100,
                       y = 0.9))

##############################################################
```

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### Activity vs. Phylogeny vs. Function

```{r, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE}
##############################################################
attach(APF3D.log)

legendtitle <- list(y=0.94,x=1.06, text="Community\nGroup\n",showarrow=F)
      
plot_ly(APF3D.log,
        x = ~Phylogenetic_Diversity, y = ~Activity_change, z = ~Functional_Diversity,
        color = ~Group,
        colors = c("#F8766D","#7CAE00", "#00BFC4", "#C77CFF"), # colors = "Set1",
        # size = ~Activity_change,
        type = "scatter3d",
        mode = "markers",
        marker = list(size = 10,
                      line = list(color = "black",
                                  width = 1)),
        text = paste("Community: ", Label,
                      "</br> Activity:", Activity_change)) %>%
  layout(scene = list(xaxis = list(title = "Phylogenetic Dissimilarity"),
                      yaxis = list(title = "EEA % change / log10"),
                      zaxis = list(title = "Functional Dissimilarity")),
         margin = list(r = 0,
                       t = 0,
                       b = 0,
                       l = 0,
                       pad = 0),
         legend = list(x = 100,
                       y = 0.9),
         annotations = legendtitle)
##############################################################
```

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# Next steps...

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### Phylogeny vs. Function, Size=EEActivity

```{r, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE}
##############################################################

# 2D plots

plot_ly(APF3D.log,
        x = ~Phylogenetic_Diversity, y = ~Functional_Diversity,
        type="scatter",
        text = paste("Community: ", APF3D.log$Label),
        mode = "markers",
        marker = list(line = list(color = "black")),
        color = ~Group,
        colors = c("#F8766D","#7CAE00", "#00BFC4", "#C77CFF"),
        size = ~Activity_change) %>%
  layout(xaxis = list(title = "Phylogenetic Dissimilarity"),
         yaxis = list(title = "Functional Dissimilarity"))

##############################################################
```

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### Phylogeny vs. Activity, Size=Functional Dissimilarity

```{r, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE}
##############################################################

# 2D plots

plot_ly(APF3D.log,
        x = ~Phylogenetic_Diversity, y = ~Activity_change,
        type="scatter",
        text = paste("Community: ", APF3D.log$Label),
        mode = "markers",
        marker = list(line = list(color = "black")),
        color = ~Group,
        colors = c("#F8766D","#7CAE00", "#00BFC4", "#C77CFF"),
        size = ~Functional_Diversity) %>%
  layout(xaxis = list(title = "Phylogenetic Dissimilarity"),
         yaxis = list(title = "EEA % change / log10"))

##############################################################
```

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### Function vs. Activity, Size=Phylogenetic Dissimilarity

```{r, echo=FALSE, fig.align="center", message=FALSE, warning=FALSE}
##############################################################

# 2D plots
plot_ly(APF3D.log,
        x = ~Functional_Diversity, y = ~Activity_change,
        type="scatter",
        text = paste("Community: ", APF3D.log$Label),
        mode = "markers",
        marker = list(line = list(color = "black")),
        color = ~Group,
        colors = c("#F8766D","#7CAE00", "#00BFC4", "#C77CFF"),
        size = ~Phylogenetic_Diversity) %>%
  layout(xaxis = list(title = "Functional Dissimilarity"),
         yaxis = list(title = "EEA % change / log10"))

##############################################################
```