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I'm trying to set the colour in R for "points" or markers in plotly with a custom palette. It doesn't work. I'm also trying to add a title to the graph, but it won't appear. In addition, I'd like to remove some elements of the legend (like the extra "z") and add a title to the legend elements. Nothing seems to work, even if it is present in the code.
library(plotly)
library(tidyverse)
set.seed(123456)
pal <- c("black", "orange", "darkgreen", "pink")
pal <- setNames(pal, levels(as.factor(c("gr1","gr2","gr3","gr4"))))
linedat = data.frame(x = rep(mean(1:50),2),
y = rep(mean(1:50),2),
z = c(0,1))
zoom = 3
pg = plotly::plot_ly(x = 1:50,
y = 1:50,
z = outer(1:50,1:50,"+")/100) %>%
add_surface(contours = list(
z = list(show = TRUE, start = 0, end = 1, size = 0.05)),
opacity = 1) %>%
add_markers(x = rnorm(50,25,5),
y = rnorm(50,25,5),
marker = list(opacity = 0.9),
type="scatter3d",
mode = "markers",inherit = FALSE,
colors = pal,
color = as.factor(sample(1:4,50,replace = T)),
z = rbinom(50,1,.5)) %>%
layout(scene=list(title = "Title won't show up????",
xaxis = list(title = 'trait1'),
yaxis = list(title = 'trait1',autorange = "reversed"),
camera = list(eye = list(x = cos(0.8*pi)*zoom, y = sin(pi*1.3)*zoom, z= 2.00)),
legend = list(title=list(text='<b> Groups </b>')))) %>%
add_trace(data=linedat, x=~x, y=~y, z=~z,
type="scatter3d", mode="lines",
line = list(color = pal[1],
width = 14),name = "Avg. data1")%>%
add_trace(data=linedat, x=~x+20, y=~y+20, z=~z,
type="scatter3d", mode="lines",
line = list(color = pal[4],
width = 14),name = "Avg. data2")
pg
See how here I'm able to set the colour of the points, but I'm not able to get the names of the colours to show in the legend (I modified the code to match what #Kat suggested):
library(plotly)
library(tidyverse)
set.seed(123456)
pal <- c("black", "orange", "darkgreen", "pink")
pal <- setNames(pal, levels(as.factor(c("gr1","gr2","gr3","gr4"))))
linedat = data.frame(x = rep(mean(1:50),2),
y = rep(mean(1:50),2),
z = c(0,1))
zoom = 3
pg = plotly::plot_ly(x = 1:50,
y = 1:50,
z = outer(1:50,1:50,"+")/100) %>%
add_surface(contours = list(
z = list(show = TRUE, start = 0, end = 1, size = 0.05)),
opacity = 1, colorbar = list(title = "Only one Z")) %>%
add_markers(x = rnorm(50,25,5),
y = rnorm(50,25,5),
marker = list(color = pal[as.factor(sample(1:4,50,replace = T))],opacity = 0.9),
type="scatter3d",
mode = "markers",inherit = FALSE,
colors = pal,
z = rbinom(50,1,.5)) %>%
layout(title = "Title that won't show",
margin = list(t = 40),
legend = list(title = list(
text = "<br>Legends deserve names, too")),
scene=list(xaxis = list(title = 'trait1'),
yaxis = list(title = 'trait1',autorange = "reversed"),
camera = list(eye = list(x = cos(0.8*pi)*zoom,
y = sin(pi*1.3)*zoom, z= 2.00)))) %>%
add_trace(data=linedat, x=~x, y=~y, z=~z,
type="scatter3d", mode="lines",
line = list(color = pal[1],
width = 14),name = "Avg. data1")%>%
add_trace(data=linedat, x=~x+20, y=~y+20, z=~z,
type="scatter3d", mode="lines",
line = list(color = pal[4],
width = 14),name = "Avg. data2");pg
Your original plot_ly call and add_trace calls can remain as is. I've included the changes needed for the layout call and added the call needed for colorbar.
The layout first.
layout(title = "Title that won't show", # <------ give my plot a name
margin = list(t = 40), # don't smash that title, either
legend = list(title = list(
text = "<br>Legends deserve names, too")), # <--- name my legend
scene=list(title = "Title won't show up????", # <- this can go away
xaxis = list(title = 'trait1'),
yaxis = list(title = 'trait1',autorange = "reversed"),
camera = list(eye = list(x = cos(0.8*pi)*zoom,
y = sin(pi*1.3)*zoom, z= 2.00)),
legend = list(title=list(text='<b> Groups </b>')))) %>%
colorbar(title = "Only one Z") # <--- give me one z colorbar title
(Some colors are different in the image; I didn't realize I had the pal object...sigh)
Update
This addresses your additional questions.
First, I'm not getting an error from the method in which I title the color bar. You'll have to share what error you're getting.
I didn't realize that it was ignoring the colors you set in markers, either. The easiest way to address this is to call that trace first. Since nothing else was declared within markers, I called opacity outside of the list, but it's fine the way you have it.
First, I commented out the setNames call, because that won't work for the marker's trace and it doesn't matter to the other traces.
library(plotly)
set.seed(123456)
pal <- c("black", "orange", "darkgreen", "pink")
# pal <- setNames(pal, levels(as.factor(c("gr1","gr2","gr3","gr4"))))
linedat = data.frame(x = rep(mean(1:50),2),
y = rep(mean(1:50),2),
z = c(0,1))
zoom = 3
I made plot_ly() empty and put all the data for the surface in that trace. I also added inherit = false so that the layout could go at the end without the data errors.
set.seed(123456)
pg = plotly::plot_ly() %>%
add_trace(inherit = F,
x = rnorm(50,25,5),
y = rnorm(50,25,5),
type="scatter3d",
mode = "markers",
opacity = .8,
colors = pal,
color = as.factor(sample(1:4, 50, replace = T)),
z = rbinom(50,1,.5)) %>%
add_surface(x = 1:50,
y = 1:50,
z = outer(1:50,1:50,"+")/100,
colorscale = "Viridis",
contours = list(
z = list(show = TRUE, start = 0, end = 1, size = 0.05)),
opacity = 1) %>%
add_trace(data=linedat, x=~x, y=~y, z=~z,
type="scatter3d", mode="lines",
line = list(color = pal[1],
width = 14),name = "Avg. data1", inherit = F) %>%
add_trace(data=linedat, x=~x+20, y=~y+20, z=~z,
type="scatter3d", mode="lines",
line = list(color = pal[4],
width = 14),name = "Avg. data2", inherit = F) %>%
The last part is the layout, but this is not different than my original answer.
layout(title = "Title that won't show", # <------ give my plot a name!
margin = list(t = 40), # don't smash that title, either
legend = list(title = list(
text = "<br>Legends deserve names, too"),
tracegroupgap = 350), # <--- name my legend!
scene=list(title = "Title won't show up????", # <--- this can go away!
xaxis = list(title = 'trait1'),
yaxis = list(title = 'trait1',autorange = "reversed"),
camera = list(eye = list(x = cos(0.8*pi)*zoom,
y = sin(pi*1.3)*zoom, z= 2.00)),
legend = list(title=list(text='<b> Groups </b>')))) %>%
colorbar(title = "Only one Z") # <--- give me one z for the title!
pg
I am trying to reproduce a graph generated via ggplotly with plot_ly. I am struggling however with the colorbar.
This is the ggploty plot that I would like to reproduce, and in particular the colorbar:
library(plotly)
X <- data.frame(w = rep(c("a", "b"), each = 8),
x = 1:16,
y = 1:16,
z = c(1, 1:13, 13, 13))
X$z_scaled <- (X$z-min(X$z))/(max(X$z)-min(X$z)) # scale to 0-1
# ggplot
gg <- ggplot(X) +
geom_point(aes(x, y, color = z_scaled, alpha = w, text = paste0(x, ", ", y))) +
scale_color_gradient2(low = '#0d71db', mid = "#dbc00d", high = '#db220d',
midpoint = .5, breaks = 0:1, limits = 0:1) +
scale_alpha_manual(name = " ", values = rep(1, nrow(X))) +
labs(color = "Z", x = "", y = "")
ggplotly(gg, type = "scattergl", tooltip = "text") %>% toWebGL()
This is what I have with plot_ly:
length_unique_vals <- length(unique(X$z))
.colors <- colorRampPalette(c('#0d71db', "#dbc00d", "#db220d"))(length_unique_vals)
.colors <- .colors[factor(X$z)]
plot_ly() %>%
add_markers(
data = X, x = ~x, y = ~y,
split = ~w,
text = ~paste0(x, ", ", y),
hoverinfo = "text",
type = "scattergl",
mode = "markers",
marker = list(
# color = ~z_scaled,
color = .colors,
# colorscale = list(c(0, .5, 1), c("#0d71db", "#dbc00d", "#db220d")),
colorscale = .colors,
hoverlabel = list(bgcolor = .colors),
colorbar = list(
title = list(text = "Z"),
len = .5,
x = 1,
y = .7
)
)
) %>%
layout(
legend = list(x = 1, y = .4, bgcolor = 'rgba(255,255,255,0.6)')
) %>% toWebGL() %>% partial_bundle(local = FALSE)
As you can see, the colorbar is not displaying correctly. I have tried multiple possibilities (commented above) without success. What am I missing?
Edit
#Kat's answer solves the colorbar issue. However, if you want to use scattergl or toWebGl you will need to fix the hoverlabel background so it remains dynamic. Here is a solution for that below building on her answer.
length_unique_vals <- length(unique(X$z))
.colors <- colorRampPalette(c('#0d71db', "#dbc00d", "#db220d"))(length_unique_vals)
.colors <- .colors[factor(X$z)]
plot_ly() %>%
add_trace(x = ~x,
y = ~y,
split = ~w, # instead of alpha or opacity
data = X,
type = "scattergl",
mode = "markers",
color = ~z_scaled, # color = var and colors = literal colors
colors = c('#0d71db', "#dbc00d", '#db220d'),
hoverlabel = list(bgcolor = .colors)) %>% # Fix hovercolor bg
layout(xaxis = list(title = "",
dtick = 4,
zeroline = F,
gridcolor = "white"), # white on gray
yaxis = list(title = "",
dtick = 4,
zeroline = F,
gridcolor = "white"), # white on gray
plot_bgcolor = "#eeeeee") %>% # gray background
colorbar(title = "Z", # colorbar title
dtick = c(0, 1), # colorbar ticks
thickness = 25) %>% # width
toWebGL() %>% partial_bundle(local = FALSE)
Edit 2
The hoverlabel bgcolor breaks down then the split factor is not ordered. This is why it needs to be ordered first.
library(plotly)
library(data.table)
X <- data.table(w = rep(c("a", "b"), 8), #not ordered
x = 1:16,
y = 1:16,
z = c(1, 1:13, 13, 13))
X[, z_scaled := (X$z-min(X$z))/(max(X$z)-min(X$z))] # scale to 0-1
# Get colors for hoverlabel bgcolor
X <- X[order(w)]
length_unique_vals <- length(unique(X$z))
.colors <- colorRampPalette(c('#0d71db', "#dbc00d", "#db220d"))(length_unique_vals)
.colors <- .colors[factor(X$z)]
plot_ly() %>%
add_trace(x = ~x,
y = ~y,
split = ~w, # instead of alpha or opacity
data = X,
type = "scattergl",
mode = "markers",
color = ~z_scaled, # color = var and colors = literal colors
colors = c('#0d71db', "#dbc00d", '#db220d'),
hoverlabel = list(bgcolor = .colors),
marker = list(size = 10)) %>% # Fix hovercolor bg
layout(xaxis = list(title = "",
dtick = 4,
zeroline = F,
gridcolor = "white"), # white on gray
yaxis = list(title = "",
dtick = 4,
zeroline = F,
gridcolor = "white"), # white on gray
plot_bgcolor = "#eeeeee") %>% # gray background
colorbar(title = "Z", # colorbar title
dtick = c(0, 1), # colorbar ticks
thickness = 25) %>% # width
toWebGL() %>% partial_bundle(local = FALSE)
Assuming you even wanted the gray background, this should work. If something isn't clear or not what you were looking for, let me know.
You don't even need the text, because you specified the default hover content.
plot_ly() %>%
add_trace(x = ~x,
y = ~y,
split = ~w, # instead of alpha or opacity
data = X,
type = "scatter",
mode = "markers",
color = ~z_scaled, # color = var and colors = literal colors
colors = c('#0d71db', "#dbc00d", '#db220d')) %>%
layout(xaxis = list(title = "",
dtick = 4,
zeroline = F,
gridcolor = "white"), # white on gray
yaxis = list(title = "",
dtick = 4,
zeroline = F,
gridcolor = "white"), # white on gray
plot_bgcolor = "#eeeeee") %>% # gray background
colorbar(title = "Z", # colorbar title
dtick = c(0, 1), # colorbar ticks
thickness = 25) # width
I'd like to do plotly chart and plot filled area shape and bars on one plot. However area shape overlaying bars. I couldn't change order of elements. Is it possible to bring bars in fron?
data <- data.frame(years = c(2005,2006,2007), values1 = c(1,2,3), values2 = c(3,3,2))
plot_ly(data, x = data$years, y=data$values1, type = 'bar') %>%
add_trace(x=data$years, y=data$values2, type = 'scatter', mode = 'lines', fill = 'tozeroy')
This is adapted from the answer by #Maximilian Peters. This code
data <- data.frame(years = c(2005,2006,2007), values1 = c(1,2,3), values2 = c(3,3,2))
plot_ly(data) %>%
add_trace(x=~years, y=~values1, type = 'bar') %>%
add_trace( x = ~years, y=~values2, type = 'scatter', mode = 'lines', fill = 'tozeroy', yaxis='y2'
) %>%
layout(title = 'Trace order Plotly R',
xaxis = list(title = ""),
yaxis = list(side = 'left', title = 'Y - Axis', overlaying = "y2"),
yaxis2 = list(side = 'right', title = "" )
)
generates this output:
I have code for a radar chart below created in the plotly package in R. The lines are straight from point to point but I would like to make them curved. I'm trying to read documentation to plotly but having trouble interpreting.
This is the code I have:
fig <- plot_ly(
type = 'scatterpolar',
r = c(1,3,2,4,1),
theta = c("A","B","C","D","E"),
fill = 'toself',
line = list(c(shape = "spline"))
)
fig %>%
layout(
polar = list(
radialaxis = list(
visible = T,
range = c(0,4)
)
),
showlegend = F
)
I would like the lines to be curved at the points.
There is no need to enclose the shape call as vector.
fig <- plot_ly(
type = 'scatterpolar',
mode = "lines+markers",
r = c(1,3,2,4,1, 1),
theta = c("A","B","C","D","E", "A"),
fill = 'toself',
line = list(shape = 'spline')
)
fig %>%
layout(
polar = list(
radialaxis = list(
visible = T,
range = c(0,4)
)
),
showlegend = F
)
To change the colors of the background and the grid lines:
fig <- plot_ly(
type = 'scatterpolar',
mode = "lines+markers",
r = c(1,3,2,4,1, 1),
theta = c("A","B","C","D","E", "A"),
fill = 'toself',
line = list(shape = 'spline')
)
fig %>%
layout(
polar = list(
bgcolor = "yellow",
radialaxis = list(
visible = T,
range = c(0,4),
gridcolor = "blue",
linecolor = "red"),
angularaxis = list(
linecolor = "darkgreen")
),
showlegend = F
)
I have the following bar in plotly and I want to :
get the x-axis title away from the axis label so they dont overlap
make the Y-axis labels bigger
bring the bar values to the top of bars
My code is :
library(plotly)
plot_ly(x = c('100-200','200-400', '400-600','600-800','800- 1000'),
y = c(12261,29637,17469,11233,17043),
name = "dd",
type = "bar",
xaxis = list(title ="tr"),
yaxis = list(title = "cc") ,
text = c(12261,29637,17469,11233,17043),textposition = 'auto') %>%
layout(
xaxis = list(tickangle=15, title = " "),
yaxis = list(title = " "))
Thanks for your comments :)
Question 1: get the x-axis title away from the axis label so they dont overlap
This problem can be solved setting proper margins with margin = list(b=100, l=100) in layout.
Question 2: make the Y-axis labels bigger.
Use xaxis = list(titlefont=list(size=30)) in layout
Question 3: bring the bar values to the top of bars.
Use add_text with textposition = 'top'
library(plotly)
x <- c('100-200','200-400', '400-600','600-800','800-1000')
y <- c(12261,29637,17469,11233,17043)
labs <- c(12261,29637,17469,11233,17043)
plot_ly(x = x, y = y,
name = "dd",
type = "bar",
xaxis = list(title ="tr"),
yaxis = list(title = "cc")) %>%
add_text(x=x, y=y, text=labs, hoverinfo='none', textposition = 'top', showlegend = FALSE,
textfont=list(size=20, color="black")) %>%
layout(margin = list(b=100, l=100),
xaxis = list(tickangle=15, title = "Lenght of exon", titlefont=list(size=30)),
yaxis = list(title = "Number of genes", titlefont=list(size=30)))
Note that your graph is not exactly reproducible with the given code at the moment, so let me know if I have made unnecessary assumptions.
TLDR: Look at the bottom if you prefer all the changes described in the question.
I would recommend not using tickangle as it screws things up a bit. Try the following. Note the use of insidetextfont and tickfont for the yaxis.
library(plotly)
x = c('100-200','200-400', '400-600','600-800','800- 1000')
y = c(12261,29637,17469,11233,17043)
plot_ly(
x = x, y = y, type = "bar", text = y, textposition = 'auto',
insidetextfont = list(color = 'white')
) %>% layout(
xaxis = list(title = "Length of exon"),
yaxis = list(title = "Number of genes", tickfont = list(size = 15))
)
If you want to make the labels lie outside the bars, then use textposition = 'outside' instead of textposition = 'auto', and get rid of the insidetextfont for the default black colour. That may end up messing with the range of the y axis and you would need to manually define the range which may be cumbersome.
plot_ly(
x = x, y = y, type = "bar", text = y, textposition = 'outside'
) %>% layout(
xaxis = list(title = "Length of exon"),
yaxis = list(
title = "Number of genes", tickfont = list(size = 15),
range = c(0, max(y) + 2000)
)
)
This gives us .
I do not recommend tickangle, but if you must, use it with margin in layout.
plot_ly(
x = x, y = y, type = "bar", text = y, textposition = 'outside'
) %>% layout(
xaxis = list(title = "Length of exon", tickangle = 15),
yaxis = list(
title = "Number of genes", tickfont = list(size = 15),
range = c(0, max(y) + 2000)
), margin = list(b=100)
)
Hope this helps.