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### Lab Tutorial: Making a 3D Figure using Plotly ###
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toy.data <- read.csv("toy.data.csv", header=TRUE)
head(toy.data)

######### Making a 3D plot with Plotly##################
#Make sure these packages are installed: plotly and RColorBrewer
## Load libraries:
library(plotly) #For making 3D plot
library(RColorBrewer) # For assigning colors

#Set colors, two methods:
colors <- brewer.pal(6, "Accent") #Accent or Set2 seem to be the best

#Manually set colors (useful when there are a lot of categories)
colors <- c("springgreen", "gold", "red3", "lightskyblue", "darkmagenta", "midnightblue")

#Assign each color to each unique "Bacteria" type
colors <- colors[as.numeric(toy.data$Bacteria)]


#Basic 3d plot with plotly
p.1 <- plot_ly(toy.data, x = ~Factor1, y = ~Factor2, z = ~Factor3, 
              color = ~Bacteria, #Each Taxa 
              colors = colors ) %>% #Assign colors according to "colors" item above
                                    # Note: Use "%>%" to pipe from one section of plot attributes to another
  add_markers() # Add markers

#Adjust the figure axes:
# Add a title to axes (note these are made up) 
#and manually set minimum/maximum to account for different ranges of each axis,
#so that they don't appear to be on the same scale
p.2 <- plot_ly(toy.data, x = ~Factor1, y = ~Factor2, z = ~Factor3, 
              color = ~Bacteria, #Each Taxa 
              colors = colors ) %>%
  add_markers() %>%
  layout(scene = list(xaxis = list(title = 'Geographic range', range = c(0,20)), #"range" sets the min/max on axis
                      yaxis = list(title = 'Size', range=c(0,10)),
                      zaxis = list(title = 'Speed', range=c(0,20)),
                      aspectratio = list(x=1, y=0.5, z=1))) #Sets the ratio of axis length



#Now make the marker sizes proportional to a characteristic ("Point_size" column)
p.3 <- plot_ly(toy.data, x = ~Factor1, y = ~Factor2, z = ~Factor3, 
               color = ~Bacteria, #Each Taxa 
               colors = colors , 
               marker = list(sizeref=0.05), opacity=0.8, #Use sizeref  if `marker.size` is set to a numerical array. Sets the scale factor used to determine the rendered size of marker points.
                                            #Opacity allows overlapping symbols to be visible. Value = 0-1.
               size = ~Point_size, sizemode="diameter") %>% #Setting size to value in column, sizemode can be diameter or area
  add_markers() %>%
  layout(scene = list(xaxis = list(title = 'Geographic range', range = c(0,20)), #"range" sets the min/max on axis
                      yaxis = list(title = 'Size', range=c(0,10)),
                      zaxis = list(title = 'Speed', range=c(0,20)),
                      aspectratio = list(x=1, y=0.5, z=1))) #Sets the ratio of axis length
##Note on transparency: "opacity" argument better when everything's a different color, "alpha" if they're the same color


##Now set symbols based on a characteristic
##Shows some options for sizemode and symbol type 
p.4 <- plot_ly(toy.data, x = ~Factor1, y = ~Factor2, z = ~Factor3, 
               color = ~Bacteria, #Each Taxa 
               colors = colors ,
               marker = list(sizeref=0.05), opacity=0.8, #Use sizeref  if `marker.size` is set to a numerical array. Sets the scale factor used to determine the rendered size of marker points.
               #Opacity allows overlapping symbols to be visible. Value = 0-1.
               size = ~Point_size, sizemode="diameter", #Setting size to value in column, sizemode can be diameter or area
               opacity=0.8,  #Opacity allows overlapping symbols to be visible. Value = 0-1.
               symbol = ~Resistance, symbols = c('circle', 'O')) %>% #Setting symbols based on "Resistance"
  add_markers() %>%
  layout(scene = list(xaxis = list(title = 'Geographic range', range = c(0,20)), #"range" sets the min/max on axis
                      yaxis = list(title = 'Size', range=c(0,10)),
                      zaxis = list(title = 'Speed', range=c(0,20)),
                      aspectratio = list(x=1, y=0.5, z=1))) #Sets the ratio of axis length



### Final step: a short, edited label 
p.5 <- plot_ly(toy.data, x = ~Factor1, y = ~Factor2, z = ~Factor3, 
               color = ~Bacteria, #Each Taxa 
               colors = colors ,
               marker = list(sizeref=0.05), opacity=0.8, #Use sizeref  if `marker.size` is set to a numerical array. Sets the scale factor used to determine the rendered size of marker points.
               #Opacity allows overlapping symbols to be visible. Value = 0-1.
               size = ~Point_size, sizemode="diameter", #Setting size to value in column, sizemode can be diameter or area
               opacity=0.8,  #Opacity allows overlapping symbols to be visible. Value = 0-1.
               symbol = ~Resistance, symbols = c('circle', 'O'), #Setting symbols based on "Resistance"
                text = paste(toy.data$Bacteria, toy.data$Resistance, sep=" "), #Sets what the hover label will say
                textposition = "top", #Sets position, there are several options
                hoverinfo = "text",
                mode = "markers + text") %>% 
  add_markers() %>%
  layout(scene = list(xaxis = list(title = 'Geographic range', range = c(0,20)), #"range" sets the min/max on axis
                      yaxis = list(title = 'Size', range=c(0,10)),
                      zaxis = list(title = 'Speed', range=c(0,20)),
                      aspectratio = list(x=1, y=0.5, z=1))) #Sets the ratio of axis length

#You can upload your plot as an interactive html file, but you must make 
#an account with Plotly first.
#Plotly can do a lot. For more information: https://plot.ly/r/

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