R: formatting plotly hover text - r

Question

I am using the R programming language. I trying to learn how to customize hover text in 3d plotly objects as seen here: https://rstudio-pubs-static.s3.amazonaws.com/441420_9a7c15988f3c4f59b2d828eb87ba1634.html
Recently, I have learned how to create a 3d plotly object for some data that I simulated :
library(Rtsne)
library(dplyr)
library(ggplot2)
library(plotly)
library(caret)
library(randomForest)
#data
a = iris
a <- unique(a)
#create two species just to make things easier
s <- c("a","b")
species<- sample(s , 149, replace=TRUE, prob=c(0.3, 0.7))
a$species = species
a$species = as.factor(a$species)
#split data into train/test, and then random forest
index = createDataPartition(a$species, p=0.7, list = FALSE)
train = a[index,]
test = a[-index,]
rf = randomForest(species ~ ., data=train, ntree=50, mtry=2)
#have the model predict the test set
pred = predict(rf, test, type = "prob")
labels = as.factor(ifelse(pred[,2]>0.5, "a", "b"))
confusionMatrix(labels, test$species)
#tsne algorithm
tsne_obj_3 <- Rtsne(test[,-5], perplexity=1, dims=3)
df_m2 <- as.data.frame(tsne_obj_3$Y)
df_m2$labels = test$species
df_m2$color = ifelse(df_m2$labels == "a", "red","blue")
df_m2$petal_length = test$Petal.Length
axis_1 = df_m2$V1
axis_2 = df_m2$V2
axis_3 = df_m2$V3
plot_ly(x=as.vector(axis_1),
y=as.vector(axis_2),
z=axis_3,
type="scatter3d",
mode="markers",
name = "Obs",
marker = list(size = 3)) %>%
add_mesh(x=as.vector(axis_1),
y=as.vector(axis_2),
z=df_m2$pred,
type = "mesh3d",
name = "Preds")
Now, I am trying to customize this plotly object so that different labels appear when you move the mouse over each point, and points corresponding to a given class all have the same color:
p <- plot_ly(type = 'scatter3d', mode = 'markers', colors = "Accent", color = df_m2$color) %>%
add_trace(
x = df_m2$V1,
y = df_m2$V2,
z = df_m2$V3,
marker = list(
size = 3),
name = df_m2$labels,
text = paste("Species: ", df_m2$labels ; "Width: ", df_m2$petal.width ; "color: ", df_m2$color" ),
showlegend = T
) %>%
add_mesh(x=as.vector(axis_1),
y=as.vector(axis_2),
z=df_m2$pred,
type = "mesh3d",
name = "Preds")
%>%
layout(
title = "none",
titlefont = list(
size = 10
),
paper_bgcolor = "#fffff8",
font = t,
xaxis = list(
zeroline = F
),
yaxis = list(
hoverformat = '.2f',
zeroline = F
)
)
p
However, there is an error here. Can someone please show me what I am doing wrong?
Thanks

Answer 1

Not sure what exactly you want to do with the predicted classes, but maybe something like this? (Color corresponds to real species, mouseover also shows prediction).
library(reprex)
reprex({
suppressPackageStartupMessages(invisible(
lapply(c("Rtsne", "dplyr", "ggplot2", "plotly", "caret", "randomForest"),
require, character.only = TRUE)))
#data
a <- unique(iris)
#create two species just to make things easier
set.seed(123)
a$species <- factor(sample(c("a", "b"), 149, replace=TRUE, prob=c(0.3, 0.7)))
#split data into train/test, and then random forest
index = createDataPartition(a$species, p=0.7, list = FALSE)
train = a[index,]
test = a[-index,]
rf <- randomForest(species ~ ., data=train, mtry=2)
#have the model predict the test set
pred <- predict(rf, test, type = "prob")
labels <- predict(rf, test)
confusionMatrix(labels, test$species)
#tsne algorithm
tsne_obj_3 <- Rtsne(test[,-5], perplexity=1, dims=3)
df_m2 <- as.data.frame(tsne_obj_3$Y)
df_m2$labels = toupper(test$species)
df_m2$pred <- labels # you did not define but call pred in plot_ly call
df_m2$color = ifelse(df_m2$labels == "A", "red", "blue")
df_m2$petal_length = test$Petal.Length
axis_1 <- df_m2$V1
axis_2 <- df_m2$V2
axis_3 <- df_m2$V3
plot_ly(type = 'scatter3d', mode = 'markers', colors = c("blue", "red"),
color = df_m2$color) %>%
add_trace(
x = df_m2$V1,
y = df_m2$V2,
z = df_m2$V3,
marker = list(size = 3),
name = df_m2$pred,
text = paste0("Species: ", df_m2$labels, "; Length: ",df_m2$petal_length, "; color: ", df_m2$color),
showlegend = TRUE) %>%
add_mesh(x=as.vector(axis_1),
y=as.vector(axis_2),
z=axis_3, # not sure what z you want here
type = "mesh3d",
name = "Preds") %>%
layout(
title = "none",
titlefont = list(size = 10),
paper_bgcolor = "#fffff8",
font = "Open Sans",
xaxis = list(zeroline = FALSE),
yaxis = list(hoverformat = '.2f', zeroline = FALSE)
)