Plotly legendgroup for subplots so a single legend controls all charts - r

I'm using plotly in r to generate a number of subplots. A toy example is shown below.
library(shiny)
library(dplyr)
library(plotly)
## Toy Example
ui <- fluidPage(
h3("Diamonds"),
plotlyOutput("plot", height = 600)
)
server <- function(input, output, session) {
# reduce down the dataset to make the example simpler
dat <- diamonds %>%
filter(clarity %in% c("I1", "IF")) %>%
mutate(clarity = factor(clarity, levels = c("I1", "IF")))
output$plot <- renderPlotly({
# Generates the chart for a single clarity
byClarity <- function(df){
Clarity <- df$clarity[1];
plot_ly(df, x = ~carat, y = ~price, color = ~cut, name = ~clarity) %>%
add_trace(
type="bar"
## Also tried adding this with no success
# legendgroup = ~cut
) %>%
layout(
barmode = "stack"
)
}
dat %>%
split(.$clarity) %>%
lapply(byClarity) %>%
subplot(nrows = NROW(.), shareX = TRUE, which_layout = "merge")
})
}
shinyApp(ui, server)
I would like to make the legends such that clicking on a 'Cut' on the legend will show/hide that 'Cut' from both charts instead of just the chart associated with that legend.
I looked at legendgroup but can't figure out how to associate it with cut instead of clarity (clarity is the grouping I'm using to make the subplots).
I also need the solution to work with raw plot_ly and not ggplotly as there are other plot_ly functionalities I need that aren't available in ggplotly.
Any help would be appreciated. I am using plotly_4.5.2, dplyr_0.5.0, and shiny_0.14.

Ok, here is a solution using ggplot2:
library(ggplot2)
library(dplyr)
library(plotly)
dat <- diamonds %>%
filter(clarity %in% c("I1", "IF")) %>%
mutate(clarity = factor(clarity, levels = c("I1", "IF")))
# Function for nice labels
k_label <- function(x) {
c(0, paste0((x)/1000,"K")[-1])
}
# ggplot
p <- ggplot(dat,aes(x=carat, y=price, fill=cut)) +
geom_bar(stat="identity") +
facet_wrap(~clarity,nrow=2, scales = "free_y") +
scale_y_continuous(labels = k_label) +
theme_minimal() + ylab("") + xlab("") +
theme(legend.title=element_blank(),
panel.grid.major.x=element_blank())
# a plotly
ggplotly(p)

Try adding legendgroup = ~cut to both traces and setting showlegend = F for one of them. Then in layout set showlegend = T
Like this:
plot_ly(df, x = ~carat, y = ~price, color = ~cut, name = ~clarity, legendgroup = ~cut, showlegend = T) %>%
add_trace( type="bar", legendgroup = ~cut, showlegend = F) %>%
layout(
barmode = "stack",showlegend = T
)

Related

How to change legend from colorbar to "regular legend", still using color gradient

Package shinyscreenshot is not able to print plotly colorbars (shiny screenshot appears with colorless legend), so I'm looking for a way to still use color gradient but display the legend as if it were factorised.
Example
Origin plot with colorbar
Goal
It doesn't mattert if there are 4, 5 or X datapoints in legend.
MWE
library(ggplot2)
library(plotly)
ggplotly(
ggplot(data=mtcars,
aes(x=mpg, y=cyl, color=qsec)) +
geom_point()
)
Plotly won't make a discrete legend for you, but you can still make it happen.
First, I assigned both the ggplot and ggplotly to objects.
plt <- ggplotly(
ggplot(data=mtcars,
aes(x=mpg, y=cyl, color=qsec)) +
geom_point()
)
g <- ggplot(data=mtcars,
aes(x=mpg, y=cyl, color=qsec)) +
geom_point()
Next, use the data behind the ggplot object, combined with mtcars, to get a color by qsec data frame, so that you know what colors go with what values.
colByVal <- cbind(ggplot_build(g)$data[[1]], mtcars) %>%
as.data.frame() %>%
select(colour, qsec) %>% arrange(qsec) %>%
group_by(colour) %>%
summarise(qsec = median(qsec)) %>% as.data.frame()
I figured that four or five values would be ideal. I just used summary to pick them. However, that's not necessary. Obviously, you can choose however many values you would like. These are the values I'll show in the legend.
parts <- summary(colByVal$qsec)
# drop the mean or median (the same color probably)
parts <- parts[-4]
Next, use DescTools::Closest to find the qsec values closest to the summary values.
vals <- lapply(parts, function(k) {
DescTools::Closest(colByVal$qsec, k)[1]
}) %>% unlist(use.names = F)
Use these qsec values and the data frame with value by color to get the colors associated with these values.
cols <- colByVal %>%
filter(qsec %in% vals) %>% select(colour) %>%
unlist(use.names = F)
Using the colors and values (legend labels), use shapes and annotations (circles and text) to rebuild the legend. There is only one other element that needs to change between each legend item, the y position of the legend entry.
ys <- seq(from = .7, by = .07, length.out = length(cols))
There are two functions: shapes and annotations. Using lapply, walk through the values, colors, and y values through these functions to create the shapes and annotations.
# create shapes
shp <- function(y, cr) { # y0, and fillcolor
list(type = "circle",
xref = "paper", x0 = 1.1, x1 = 1.125,
yref = "paper", y0 = y, y1 = y + .025,
fillcolor = cr, yanchor = "center",
line = list(color = cr))
}
# create labels
ano <- function(ya, lab) { # y and label
list(x = 1.13, y = ya + .035, text = lab,
xref = "paper", yref = "paper",
xanchor = "left", yanchor = 'top',
showarrow = F)
}
# the shapes list
shps <- lapply(1:length(cols),
function(j) {
shp(ys[j], cols[j])
})
# the labels list
labs <- lapply(1:length(cols),
function(i) {
ano(ys[i], as.character(vals[i]))
})
When you use ggplotly, for some reason it ends an empty shape to the ggplotly object. This interferes with the ability to call for shapes in layout (which is the proper method). You have to force the issue with shapes. Additionally, the legend bar needs to go away. Once you drop the legend bar, Plotly will adjust the plot margins. The legend created with shapes and annotations will be hidden if you don't add the margins back.
# ggplot > ggplotly adds an empty shape; this conflicts with calling it in
# layout(); we'll replace 'shapes' first
plt$x$layout$shapes <- shps
plt %>% hide_colorbar() %>%
layout(annotations = labs, showlegend = F,
margin = list(t = 30, r = 100, l = 50, b = 30, pad = 3))
All of that code in one chunk:
library(tidyverse)
library(plotly)
# original plot
plt <- ggplotly(
ggplot(data=mtcars,
aes(x=mpg, y=cyl, color=qsec)) +
geom_point()
)
g <- ggplot(data=mtcars,
aes(x=mpg, y=cyl, color=qsec)) +
geom_point()
# color by qsec values frame
colByVal <- cbind(ggplot_build(g)$data[[1]], mtcars) %>%
as.data.frame() %>%
select(colour, qsec) %>% arrange(qsec) %>%
group_by(colour) %>%
summarise(qsec = median(qsec)) %>% as.data.frame()
parts <- summary(colByVal$qsec)
# drop the mean or median (the same color probably)
parts <- parts[-4]
vals <- lapply(parts, function(k) {
DescTools::Closest(colByVal$qsec, k)[1]
}) %>% unlist(use.names = F)
cols <- colByVal %>%
filter(qsec %in% vals) %>% select(colour) %>%
unlist(use.names = F)
ys <- seq(from = .7, by = .07, length.out = length(cols))
# create shapes
shp <- function(y, cr) { # y0, and fillcolor
list(type = "circle",
xref = "paper", x0 = 1.1, x1 = 1.125,
yref = "paper", y0 = y, y1 = y + .025,
fillcolor = cr, yanchor = "center",
line = list(color = cr))
}
# create labels
ano <- function(ya, lab) { # y and label
list(x = 1.13, y = ya + .035, text = lab,
xref = "paper", yref = "paper",
xanchor = "left", yanchor = 'top',
showarrow = F)
}
# the shapes list
shps <- lapply(1:length(cols),
function(j) {
shp(ys[j], cols[j])
})
# the labels list
labs <- lapply(1:length(cols),
function(i) {
ano(ys[i], as.character(vals[i]))
})
# ggplot > ggplotly adds an empty shape; this conflicts with calling it in
# layout(); we'll replace 'shapes' first
plt$x$layout$shapes <- shps
plt %>% hide_colorbar() %>%
layout(annotations = labs, showlegend = F,
margin = list(t = 30, r = 100, l = 50, b = 30, pad = 3))
This is only a partial answer; you can change the shape and text of the legend while maintaining its gradient by using a combination of scale_color_continuous and guides(color = guide_legend()), but this will only show up as a ggplot object. For some reason, the legend disappears when you add the plot to ggplotly(), the legend disappears. I suspect that arguments specific to the legend may need to be added to ggplotly() directly.
library(tidyverse)
library(plotly)
data(mtcars)
p <- ggplot(mtcars, aes(x = mpg, y = cyl, color = qsec)) +
geom_point() +
scale_color_continuous(breaks = c(15, 17.5, 20, 22.5)) +
guides(color = guide_legend(
reverse = T,
override.aes = list(shape = 19, size = 8))) +
theme(legend.position = "right")
p
p2 <- ggplotly(p) %>% layout(showlegend = T)
p2

boxplot annotation to outliers using r plotly

Using the iris dataset below how do I get the ID of the flower on hover of the outliers
library(plotly)?
I've tried something like:
iris_ids <- iris %>%
mutate(id = rownames(iris))
plot_ly(iris, y = ~Sepal.Length, x= ~Species, type = 'box') %>%
layout(title = 'Box Plot',
xaxis = list(title = "cond", showgrid = F),
yaxis = list(title = "rating"),
annotations = list(
x = boxplot.stats(Species)$out,
# use boxplot.stats() to get the outlier's y coordinate
y = boxplot.stats(Sepal.Length)$out,
# I want the ID of the flower
# of the outliers
text = c("ID:", id),
showarrow = FALSE,
xanchor = "right"
)
) %>%
config(displayModeBar = FALSE)
And also tried using the ggplotly wrapper:
ggplotly(
ggplot(iris_id, aes(x = Species, y = Sepal.Length)) +
geom_boxplot()
) %>%
#....what goes here....
I prefer the second way because I'm more comfortable with theming in ggplot2 but I'm open to any and all suggestions!! Thank you.
Try this approach, for sure you can customize further:
library(ggplot2)
library(plotly)
library(dplyr)
#Data
iris_ids <- iris %>%
mutate(id = rownames(iris))
#Plot
gg <- ggplotly(
ggplot(iris_ids, aes(x = Species, y = Sepal.Length)) +
geom_boxplot()
)
hoverinfo <- with(iris_ids, paste0("id: ", id, "</br></br>",
"Sepal.Length: ", Sepal.Length, "</br>"))
gg$x$data[[1]]$text <- hoverinfo
gg$x$data[[1]]$hoverinfo <- c("text", "boxes")
gg
Output:

R plotly histogram hover text

This is my code. Just a simple historgram. But what I wanted to do is to customize the hover text so that when I hover, it will display all species included in that histogram bar. Can you help me?
iris %>%
plot_ly(x=~Sepal.Length, color=~Sepal.Width, text=~Species) %>%
add_histogram()
Here's the output. But when I hover it seems the text is only displaying the first species in the table.
plotly_hist
I'm not sure whether this is possible. Probably you are demanding too much from plotly. After trying some options I think there are two ways to go if you want the different Species to show up in the tooltip:
First option is to use a stacked histogram using hovermode = "unified" like so:
library(plotly)
fig <- plot_ly()
fig <- fig %>% add_trace(data = filter(iris, Species == "setosa"),
x = ~Sepal.Length,
color = ~Species,
text = ~Species,
type='histogram',
bingroup=1, showlegend = FALSE)
fig <- fig %>% add_trace(data = filter(iris, Species == "versicolor"),
x = ~Sepal.Length,
color = ~Species,
text = ~Species,
type='histogram',
bingroup=1, showlegend = FALSE)
fig <- fig %>% add_trace(data = filter(iris, Species == "virginica"),
x = ~Sepal.Length,
color = ~Species,
text = ~Species,
type='histogram',
bingroup=1, showlegend = FALSE)
fig <- fig %>% layout(
hovermode="unified",
barmode="stack",
bargap=0.1)
fig
The second option would be to make the computations yourself, i.e. binning and summarising and to make a bar chart of the counts.
iris %>%
mutate(Sepal.Length.Cut = cut(Sepal.Length, breaks = seq(4, 8, .5), right = FALSE)) %>%
group_by(Sepal.Length.Cut, Species) %>%
summarise(n = n(), Sepal.Width = sum(Sepal.Width)) %>%
tidyr::unite("text", Species, n, sep = ": ", remove = FALSE) %>%
summarise(n = sum(n), Sepal.Width = sum(Sepal.Width) / n, text = paste(unique(text), collapse = "\n")) %>%
plot_ly(x = ~Sepal.Length.Cut, y = ~n, text = ~text) %>%
add_bars(marker = list(colorscale = "Rainbow"), hovertemplate = "%{y}<br>%{text}")
Edit A third option would be to use ggplotly(). This way it is an easy task to add annotations displayling the total numbers per bin. This way we can make use of the stats layers in ggplot2 which will do all the computations. To the best of my knowledge that couldn't be done that easily using "pure" plotly.
library(plotly)
ggplot(iris, aes(Sepal.Length, fill = Species)) +
stat_bin(breaks = seq(4, 8, .5), closed = "left") +
stat_bin(breaks = seq(4, 8, .5), closed = "left", geom = "text", mapping = aes(Sepal.Length, label = ..count..), inherit.aes = FALSE, vjust = -.5) +
theme_light()
ggplotly()

How to remove duplicate legend entries w/ plotly subplots()

How can I remove the duplicates in my legend when using plotly's subplots()?
Here is my MWE:
library(plotly)
library(ggplot2)
library(tidyr)
mpg %>%
group_by(class) %>%
do(p = plot_ly(., x = ~cyl, y = ~displ, color = ~trans, type = 'bar')) %>%
subplot(nrows = 2, shareX = TRUE, titleX = TRUE) %>%
layout(barmode = 'stack')
plotly does not have facet like ggplot2 so it will add legend for each subplot or you can turn it off for some of them.
Here we do not have a layer with all the ~class entries nor two plots with no intersection in class which their combination also covers all of them. In that case, we could set showlegend to TRUE for those specific plot(s) and set it to FALSE for the rest and also set the legendgroup to trans so we get a unique but also complete legend.
As I said, here we do not have that special case. So What I can think of are two possibilities:
Adding the whole data (duplicating whole dataframe) and assigning class of All to them. Then plotting that along with original data but keep the legend only for class == All.
Using ggplot::facet_wrap and then ggplotly to make a plotly object. However, this would cause some issues with x-axis (compare ggplot object to plotly ones).
library(plotly)
library(ggplot2)
library(dplyr)
ly_plot <- . %>%
plot_ly(x = ~cyl, y = ~displ, color = ~trans,
type = 'bar', showlegend = ~all(legendC)) %>%
add_annotations(
text = ~unique(class),
x = 0.5,
y = 1,
yref = "paper",
xref = "paper",
xanchor = "middle",
yanchor = "top",
showarrow = FALSE,
font = list(size = 15))
mpg %>%
mutate(class= "_All_") %>%
rbind(.,mpg) %>%
mutate(legendC = (class == "_All_")) %>%
group_by(class) %>%
do(p = ly_plot(.)) %>%
subplot(nrows = 2, shareX = TRUE, titleX = TRUE) %>%
layout(barmode = 'stack')
#> Warning in RColorBrewer::brewer.pal(N, "Set2"): n too large,
#> allowed maximum for palette Set2 is 8
#> Returning the palette you asked for with that many colors
p <- ggplot(data = mpg, aes(x=cyl, y=displ, fill=trans))+
geom_bar(stat="identity") +
facet_wrap(~class)
p
ggplotly(p) #seems for this we should also set "colour = trans"
Another workaround using the tidyverse. The following steps are added to the original MWE:
Convert the trans column to a factor.
Use tidyr's complete to fill (non-NA) dummy values for the missing factor levels in each class group.
Follow M-M's suggestion setting showlegend to TRUE for a single group and legendgroup to trans to link the legend entries between subplots.
library(plotly)
library(tidyverse)
mpg %>%
mutate_at("trans", as.factor) %>%
group_by(class) %>%
group_map(.f = ~{
## fill missing levels w/ displ = 0, cyl = first available value
complete(.x, trans, fill = list(displ = 0, cyl = head(.x$cyl, 1))) %>%
plot_ly(x = ~cyl, y = ~displ, color = ~trans, colors = "Paired", type = "bar",
showlegend = (.y == "2seater"), legendgroup = ~trans) %>%
layout(yaxis = list(title = as.character(.y)), barmode = "stack")
}) %>%
subplot(nrows = 2, shareX = TRUE, titleY = TRUE)

How can I combine a line and scatter on same plotly chart?

The two separate charts created from data.frame work correctly when created using the R plotly package.
However,
I am not sure how to combine them into one (presumably with the add_trace function)
df <- data.frame(season=c("2000","2000","2001","2001"), game=c(1,2,1,2),value=c(1:4))
plot_ly(df, x = game, y = value, mode = "markers", color = season)
plot_ly(subset(df,season=="2001"), x = game, y = value, mode = "line")
Thanks in advance
The answer given by #LukeSingham does not work anymore with plotly 4.5.2.
You have to start with an "empty" plot_ly() and then to add the traces:
df1 <- data.frame(season=c("2000","2000","2001","2001"), game=c(1,2,1,2), value=c(1:4))
df2 <- subset(df, season=="2001")
plot_ly() %>%
add_trace(data=df1, x = ~game, y = ~value, type="scatter", mode="markers") %>%
add_trace(data=df2, x = ~game, y = ~value, type="scatter", mode = "lines")
here is a way to do what you want, but with ggplot2 :-) You can change the background, line, points color as you want.
library(ggplot2)
library(plotly)
df_s <- df[c(3:4), ]
p <- ggplot(data=df, aes(x = game, y = value, color = season)) +
geom_point(size = 4) +
geom_line(data=df_s, aes(x = game, y = value, color = season))
(gg <- ggplotly(p))
There are two main ways you can do this with plotly, make a ggplot and convert to a plotly object as #MLavoie suggests OR as you suspected by using add_trace on an existing plotly object (see below).
library(plotly)
#data
df <- data.frame(season=c("2000","2000","2001","2001"), game=c(1,2,1,2),value=c(1:4))
#Initial scatter plot
p <- plot_ly(df, x = game, y = value, mode = "markers", color = season)
#subset of data
df1 <- subset(df,season=="2001")
#add line
p %>% add_trace(x = df1$game, y = df1$value, mode = "line")

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