R Plotly jittered boxplot with NAs width - r

Question

I am plotting the grouped boxplot with jittering with the following function:
plot_boxplot <- function(dat) {
# taking one of each joine_group to be able to plot it
allx <- dat %>%
mutate(y = median(y, na.rm = TRUE)) %>%
group_by(joined_group) %>%
sample_n(1) %>%
ungroup()
p <- dat %>%
plotly::plot_ly() %>%
# plotting all the groups 1:20
plotly::add_trace(data = allx,
x = ~as.numeric(joined_group),
y = ~y,
type = "box",
hoverinfo = "none",
boxpoints = FALSE,
color = NULL,
opacity = 0,
showlegend = FALSE) %>%
# plotting the boxes
plotly::add_trace(data = dat,
x = ~as.numeric(joined_group),
y = ~y,
color = ~group1,
type = "box",
hoverinfo = "none",
boxpoints = FALSE,
showlegend = FALSE) %>%
# adding ticktext
layout(xaxis = list(tickvals = 1:20,
ticktext = rep(levels(dat$group1), each = 4)))
p <- p %>%
# adding jittering
add_markers(data = dat,
x = ~jitter(as.numeric(joined_group), amount = 0.2),
y = ~y,
color = ~group1,
showlegend = FALSE)
p
}
The problem is that when some of the levels have NA as y variable the width of the jittered boxes changes. Here is an example:
library(plotly)
library(dplyr)
set.seed(123)
dat <- data.frame(group1 = factor(sample(letters[1:5], 100, replace = TRUE)),
group2 = factor(sample(LETTERS[21:24], 100, replace = TRUE)),
y = runif(100)) %>%
dplyr::mutate(joined_group = factor(
paste0(group1, "-", group2)
))
# do the plot with all the levels
p1 <- plot_boxplot(dat)
# now the group1 e is having NAs as y values
dat$y[dat$group1 == "e"] <- NA
# create the plot with missing data
p2 <- plot_boxplot(dat)
# creating the subplot to see that the width has changed:
subplot(p1, p2, nrows = 2)
The problem is that the width of boxes in both plots is different:
I've realised that the boxes have the same size without jittering so I know that the jittering is "messing" with the width but I don't know how to fix that.
Does anyone know how to make the width in both jittered plots exactly the same?

Answer 1

I see two separate plot shifts:
due to jittering
due to NAs
First can be solved by declaring new jitter function with fixed seed
fixed_jitter <- function (x, factor = 1, amount = NULL) {
set.seed(42)
jitter(x, factor, amount)
}
and using it instead of jitter in add_markers call.
Second problem can be solved by assigning -1 instead of NA and setting
yaxis = list(range = c(0, ~max(1.1 * y)))
as a second parameter to layout.