Plotting 3d point cloud coordinates in three panels

[imagejan]

I'd like to plot a set of 3d point coordinates (x,y,z) as three 2d scatter plot panels in an "orthogonal view":

xy	zy
xz

As a minimal example, let's consider the following data frame:

x <- c(0.9, 1.1, 1.0)
y <- c(2.0, 1.9, 2.1)
z <- c(3.1, 2.9, 3.0)

df <- data.frame(x,y,z)

Now, I'd like to create three plots, such as:

p1 <- ggplot(df, aes(x=x, y=y)) +
+ geom_point() +
+ theme_minimal()

p2 <- ggplot(df, aes(x=z, y=y)) +
+ geom_point() +
+ theme_minimal()

p3 <- ggplot(df, aes(x=x, y=z)) +
+ geom_point() +
+ theme_minimal()

... and arrange them in a way that the x and y axes align.
Is that something I can do using facets, and if so, how?

[ron]

Hi and welcome,

I've actually been playing with something along these lines myself recenlty (a customised pairs plot in my case), and I'd suggest using GGally::ggmatrix to create your array of plots:

x <- c(0.9, 1.1, 1.0)
y <- c(2.0, 1.9, 2.1)
z <- c(3.1, 2.9, 3.0)
df <- data.frame(x,y,z)

# Contains ggmatrix function...
library(GGally)
#> Loading required package: ggplot2

xy <- ggplot(df)+geom_point(aes(x=x,y=y))
zy <- ggplot(df)+geom_point(aes(x=z,y=y))
xz <- ggplot(df)+geom_point(aes(x=x,y=z))

mm <- ggmatrix(list(xy,zy,xz,NULL),nrow=2,ncol=2)
mm

^{Created on 2019-04-04 by the reprex package (v0.2.1)}

Ron.

[martin.R]

If you wish to align different plots then there are packages like cowplot, lemon and patchwork.

An alternative to ron's solution would be to use ggplot2's facets:

library(tidyverse)

x <- c(0.9, 1.1, 1.0)
y <- c(2.0, 1.9, 2.1)
z <- c(3.1, 2.9, 3.0)

df <- data.frame(x,y,z)

df <- bind_rows(
  df %>% select(axis1 = x, axis2 = y) %>% mutate(axes = "xy"), 
  df %>% select(axis1 = x, axis2 = z) %>% mutate(axes = "xz"), 
  df %>% select(axis1 = y, axis2 = z) %>% mutate(axes = "yz")
)

p <- ggplot(df, aes(x = axis1, y = axis2)) + 
  geom_point() + 
  facet_wrap(vars(axes), scales = "free")

You can play with the scales argument to suit your requirements.

[andresrcs]

Building on Martin's answer you can arrange the facets this way

df <- df %>% mutate(axes = factor(axes, levels = c("xy", "yz", "xz")))

ggplot(df, aes(x = axis1, y = axis2)) +
    geom_point() +
    facet_wrap(vars(axes), scales = "free", ncol = 2)

[imagejan]

I ended up using the multiplot function described here:

Multiple graphs on one page (ggplot2)

... mainly for the reason that it allows to set a layout adjusting the relative size of the xy plot and the z axes of the other two plots.

See here for an example usage:

Register pixel shift in 2 channel images of beads

I noticed that this function (multiplot) apparently proliferated into a few different R packages, and wondered if there is a specific reason why it's not integrated centrally in one of the ggplot or gg* packages...

---

I also figured that another option to achieve this combined plot would be the patchwork package by @thomasp85:

GitHub - thomasp85/patchwork: The Composer of ggplots

... but I refrained from using it just now in a workflow I'm going to share, because it's not yet deployed to CRAN, and requires installation from GitHub. Are there any plans to put it on CRAN soon?

[mara]

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Thanks

[thomasp85]

patchwork will hopefully get on CRAN sometimes this year...