position_jitterx: Jitter points to avoid overplotting, and the whole points can...

In YuLab-SMU/ggtreeExtra: An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

Jitter points to avoid overplotting, and the whole points can be shifted vertically or horizontally

Description

This is the extension of 'position_jitter' of ggplot2, points are randomly shifted up and down and/or left and right. In addition, the whole points layer can be shifted by the 'hexpand' or 'vexpand' parameter. Counterintuitively adding random noise to a plot can sometimes make it easier to read. Jittering is particularly useful for small datasets with at least one discrete position.

Usage

position_jitterx(
  width = NULL,
  height = NULL,
  hexpand = NA,
  vexpand = NA,
  seed = NA
)

Arguments

width, height	Amount of vertical and horizontal jitter. The jitter is added in both positive and negative directions, so the total spread is twice the value specified here. If omitted, defaults to 40% of the resolution of the data: this means the jitter values will occupy 80% of the implied bins. Categorical data is aligned on the integers, so a width or height of 0.5 will spread the data so it's not possible to see the distinction between the categories.
hexpand, vexpand	The distance to be shifted vertically or horizontally, default is NA.
seed	A random seed to make the jitter reproducible. Useful if you need to apply the same jitter twice, e.g., for a point and a corresponding label. The random seed is reset after jittering. If NA (the default value), the seed is initialised with a random value; this makes sure that two subsequent calls start with a different seed. Use NULL to use the current random seed and also avoid resetting

Examples

library(ggtree)
library(treeio)
library(ggplot2)
set.seed(1024)
tr <- rtree(10)

df <- data.frame(id=tr$tip.label, group=rep(c("A", "B"),5))
dat <- data.frame(id=rep(tr$tip.label, 8), value=rnorm(80, 0.5, 0.15))
dt <- merge(dat, df, by.x="id", by.y="id")
p1 <- ggtree(tr) %<+% df +
      geom_tiplab(
          align=TRUE,
          linesize=.1,
          size=3
      ) 

gf1 <- geom_fruit(data=dat,
                  geom=geom_boxplot,
                  mapping=aes(x=value, y=id),
                  orientation="y",
                  offset=0.1,
                  pwidth=0.9

         )
set.seed(1024)
gf2 <- geom_fruit(
          data=dat,
          geom=geom_point,
          mapping=aes(x=value, y=id, color=group),
          offset=0.1,
          pwidth=0.9,
          position= position_jitterx(height=0.3),
          axis.params=list(axis="x", text.size=2),
          grid.params=list()
          )

p2 <- p1 + geom_fruit_list(gf1, gf2)
p2

YuLab-SMU/ggtreeExtra documentation built on Nov. 8, 2024, 6:28 p.m.