CODEWITHSUNDEEP
rggplot2shinyplotlygeom-text
Komal Rathi
Komal Rathi

Reputation: 4274

Overlapping points and text with plotly in Rshiny

I am using plotly with Rshiny to create a scatter plot with text labels. Below is a reproducible example:

library(ggplot2)
library(plotly)
dat <- data.frame(LongExpressionValue = rnorm(1:100), 
                  LongMethylationValue = rnorm(1:100), 
                  LongCopyNumberValue = rnorm(1:100))

rownames(dat) <- paste0('n',seq(1:100))

# ggplot
p <- ggplot(data = dat, aes(x = LongExpressionValue, y = LongMethylationValue)) + 
  geom_point(size = 2) + geom_smooth(method = lm) +
  geom_text(aes(label = rownames(dat)), vjust=-1.5, size = 3)

# ggplotly
ggplotly(p)

This creates a plot like:

enter image description here

How do I adjust my geom_text options so that the labels appear above and not overlapping the points? I do want to retain my ggplot code for it to be used across applications.

Thanks!

Upvotes: 5

Views: 5398

Answers (3)

Shape
Shape

Reputation: 2952

Try this:

plot_ly(
    data = dat, 
    x = ~LongExpressionValue, 
    y = ~LongMethylationValue, 
    text = rownames(dat), 
    marker = list(size = 10), 
    mode = "markers+text",
    textposition = 'top center'
)

it's not worth working too hard at ggplot2 when you can go directly to the source. this is invaluable: https://plot.ly/r/reference/

Everything in plot_ly or in layout is a list of lists, so you can set your parameters easily (notice marker = list(size = 10))

EDIT: A slightly more complicated one showing the power of hoverinfo + text together:

plot_ly(
    data = dat, 
    x = ~LongExpressionValue, 
    y = ~LongMethylationValue, 
    text = paste0(rownames(dat), 
                      '<br>A:', 1:nrow(dat), #Examples of additional text
                      '<br>B:', sample(nrow(dat))), #Examples of additional text
        hoverinfo = 'text+x+y',
        marker = list(size = 10), 
        mode = "markers+text",
        textposition = 'top right')

Upvotes: 3

Georg
Georg

Reputation: 61

If you would like to stay in ggplot2 you have to append a textposition element to the plotly_build list. textposition is missing in the original plotly_build even if hjust and vjust options are set.

So this works:

#devtools::install_github("ropensci/plotly") # if not already done
library(ggplot2)
library(plotly) 
dat <- data.frame(LongExpressionValue = rnorm(1:100),
              LongMethylationValue = rnorm(1:100),
              LongCopyNumberValue = rnorm(1:100))

rownames(dat) <- paste0('n',seq(1:100))  

gg <- ggplot(data = dat, aes(x = LongExpressionValue, y =LongMethylationValue)) + 
geom_point(size = 1) +
geom_smooth(method = lm) +
geom_text(aes(label = rownames(dat)), size = 3)

p <- plotly_build(gg)

length<-length(p$x$data)
invisible(lapply(1:length, function(x) p$x$data[[x]]<<-c(p$x$data[[x]], textposition ='top center')))

p

Upvotes: 1

MLavoie
MLavoie

Reputation: 9836

If you want to stick with ggplot2 and keep your smooth line, you could increase slightly the size of your point and add your label inside each point:

p <- ggplot(data = dat, aes(x = LongExpressionValue, y = LongMethylationValue)) + 
  geom_point(size = 7) + geom_smooth(method = lm) +
  geom_text(aes(label = rownames(dat)), size = 2, color="white")

# ggplotly
ggplotly(p)

enter image description here

Upvotes: 1

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