r - How to plot a hybrid boxplot: half boxplot with jitter points on the other half?

Question

I'm trying to make a similar plot to Fig. 2d-f in an article published on Nature this year. It's basically a half boxplot with points on the other half.

Can anyone give me some hints? Thank you very much!

These are my data and code which produced full boxes with points inside

require(magrittr)
require(tidyverse)

dat <- structure(list(p1 = c(0.0854261831077604, 0.408418657218253, 
  0.577793646477315, 0.578028229977424, 0.48933166218204, 0.53117814324334, 
  0.526653494462464, 0.00687616283435221, 0.444300425796509, 0.00287319455358522, 
  0.949821402532831, 0.96832469523368, 0.953281969982759, 0.360125244759434, 
  0.407921095422844, 0.885776732104954, 0.159882184516691, 0.911094990767761, 
  0.0444367172734037, 0.144888951725151, 0.508858686640707, 0.694913731085945, 
  0.117270366119258, 0.78227546070467, 0.980457304886186, 0.711464034564424, 
  0.753944466390685, 0.0474210438747038, 0.00344183466223558, 0.0290017465534545, 
  0.75092385236303, 0.868873921257987, 0.744396990487425, 0.0140007244233847, 
  0.0332266395043963, 0.482897084793009, 0.0535516646483004, 0.452926358923891, 
  0.0144057727301603, 0.171918034525543), p2 = c(0.101262675229211, 
  0.196913109208586, 0.37814311161382, 0.0677625689405156, 0.12517090579686, 
  0.409083554335168, 0.158886941347288, 0.847394861862651, 0.180560031076741, 
  0.967122694294885, 0.000901627067665116, 0.00039495110143705, 
  9.70707318411806e-05, 0.546200038486894, 0.435475454787648, 5.95555269800323e-06, 
  0.0178837768834925, 8.42690065415846e-06, 0.00777059697751842, 
  0.0020397073541544, 0.486699073016371, 0.283679673247571, 0.857183359146641, 
  0.200712003853458, 0.0164911141652784, 0.0542250670734297, 0.232340206984506, 
  0.948523714169708, 0.169881661474024, 0.968983592882272, 0.00250367590158291, 
  0.000792323746977033, 0.000185068166140097, 0.0193600071757997, 
  0.114775271592724, 4.65931778380389e-05, 0.000754760900847164, 
  2.07521623816406e-05, 0.00782764273312856, 0.00276993826117348
  ), p3 = c(0.0118642223785376, 0.0267362912322735, 6.60753171741111e-08, 
  0.053576051466652, 0.00375873110094442, 9.85095078844696e-08, 
  0.0525436528683484, 0.0193735809639814, 8.44717454802822e-07, 
  0.00608007737576027, 0.0205563904131287, 0.0104638062130591, 
  0.0249997053664864, 0.0587924727726031, 0.0443600964770995, 0.067125687916273, 
  0.758612877724648, 0.0618158334848203, 0.0251025592849138, 0.790905778949543, 
  0.00126904829915329, 0.00760772364901772, 0.00119821088328392, 
  0.0115117347754715, 0.000863676435448072, 0.000996891439583434, 
  0.0115279148630096, 0.00249122388568909, 5.21508620418823e-05, 
  0.00144050407848742, 0.120373444447631, 0.0534773096149069, 0.110284261289338, 
  0.571243879053544, 0.438152084363961, 0.364887514202121, 0.696293189762153, 
  0.414870716968937, 0.0557358576822093, 0.783929426716999), p4 = c(0.000107231042599948, 
  0.000379648762557529, 8.25102162601208e-06, 0.000343829024899591, 
  0.000140680688077216, 1.90076798696051e-06, 0.000214507212681323, 
  1.38587688080716e-05, 3.48104084092359e-06, 6.50782599216903e-07, 
  0.0114584884733498, 0.00652170746426181, 0.0143309604192116, 
  0.0275718029789144, 0.0352327288308957, 0.022950800779703, 0.0569939247302654, 
  0.0190248244391564, 0.0305921420687752, 0.00589871320676732, 
  0.000805515847378872, 1.97674357551495e-05, 8.30853708305541e-06, 
  1.32462751169762e-06, 4.8731965929686e-05, 0.0057411315642433, 
  4.82406700397824e-05, 0.000204633566379066, 0.0552263911781015, 
  0.000181994007177494, 0.0585729576787707, 0.0273685460128338, 
  0.0568746134466117, 0.299309335625926, 0.278980446497419, 0.105600715225359, 
  0.176549247514501, 0.101420411455169, 0.01003894550707, 0.0010803018725911
  ), p5 = c(0.786823338804824, 0.151956168584644, 0.0433468890359269, 
  0.19556481029922, 0.380808150243027, 0.0389798680141623, 0.260481184897901, 
  0.101147673996922, 0.0184624278061585, 0.0222416874775066, 0.000113517761014704, 
  0.00329593083795693, 0.000476682365422989, 0.00571997662739322, 
  0.0697473913851358, 0.0216803412883361, 0.00631472476841249, 
  0.00628215584877364, 0.540944692186543, 0.0135127011440213, 0.00235752761214414, 
  3.10282042735927e-06, 0.0239147204208516, 4.97334784773176e-05, 
  0.00213837866453402, 0.000212207014031345, 0.00180443364400107, 
  8.15954685083038e-05, 0.00445169398173509, 0.000391265642772285, 
  0.0676128522356959, 0.0494864355994384, 0.0882575475549674, 0.0960799089263987, 
  0.134853114895623, 0.0465661014986807, 0.0728456746626632, 0.0307607877988244, 
  0.476388236185883, 0.00831263646470973), p6 = c(0.0145163494370677, 
  0.215596124993685, 0.00070803577599434, 0.104724510291289, 0.000789869989050939, 
  0.0207564351298348, 0.00122021921131791, 0.0251938615732845, 
  0.356672789562296, 0.00168169551566413, 0.0171485737520108, 0.0109989091496048, 
  0.00681361113427885, 0.00159046437476052, 0.00726323309637717, 
  0.00246048235803604, 0.000312511376490686, 0.00177376855883463, 
  0.351153292208846, 0.0427541476203625, 1.01485842454486e-05, 
  0.0137760017612841, 0.000425034892882118, 0.0054497425604112, 
  7.93882623673471e-07, 0.227360668344289, 0.000334737447758259, 
  0.0012777890350116, 0.766946267841861, 8.96835836820999e-07, 
  1.32173732897771e-05, 1.46376785664669e-06, 1.51905551715105e-06, 
  6.14479494697213e-06, 1.24431458762028e-05, 1.99110299298599e-06, 
  5.46251153509928e-06, 9.72690797485877e-07, 0.435603545161549, 
  0.0319896621589845), type = c("small", "small", "small", "small", 
  "small", "small", "small", "small", "small", "small", "small", 
  "small", "small", "small", "small", "small", "small", "small", 
  "small", "small", "big", "big", "big", "big", "big", "big", "big", 
  "big", "big", "big", "big", "big", "big", "big", "big", "big", 
  "big", "big", "big", "big"), loc = c("abro", "abro", "abro", 
  "abro", "abro", "abro", "abro", "abro", "abro", "abro", "dome", 
  "dome", "dome", "dome", "dome", "dome", "dome", "dome", "dome", 
  "dome", "abro", "abro", "abro", "abro", "abro", "abro", "abro", 
  "abro", "abro", "abro", "dome", "dome", "dome", "dome", "dome", 
  "dome", "dome", "dome", "dome", "dome")), .Names = c("p1", "p2", 
  "p3", "p4", "p5", "p6", "type", "loc"), class = c("tbl_df", "tbl", 
  "data.frame"), row.names = c(NA, -40L))
glimpse(dat)
#> Observations: 40
#> Variables: 8
#> $ p1   <dbl> 0.085426183, 0.408418657, 0.577793646, 0.578028230, 0.489...
#> $ p2   <dbl> 1.012627e-01, 1.969131e-01, 3.781431e-01, 6.776257e-02, 1...
#> $ p3   <dbl> 1.186422e-02, 2.673629e-02, 6.607532e-08, 5.357605e-02, 3...
#> $ p4   <dbl> 1.072310e-04, 3.796488e-04, 8.251022e-06, 3.438290e-04, 1...
#> $ p5   <dbl> 7.868233e-01, 1.519562e-01, 4.334689e-02, 1.955648e-01, 3...
#> $ p6   <dbl> 1.451635e-02, 2.155961e-01, 7.080358e-04, 1.047245e-01, 7...
#> $ type <chr> "small", "small", "small", "small", "small", "small", "sm...
#> $ loc  <chr> "abro", "abro", "abro", "abro", "abro", "abro", "abro", "...

Convert data to long format

dat_long <- dat %>%  
  gather(key, value, 1:6) %>% 
  mutate(loc = factor(loc, levels = c("abro", "dome")),
         type = factor(type),
         key = factor(key))

Plot boxplot with points

ggplot(dat_long, aes(x = type, y = value, color = key)) +
  facet_grid(loc ~ key) +
  geom_point(position = position_jitter(width = 0.3), alpha = 0.3, size = 2) +
  geom_boxplot(outlier.color = NA) +
  theme_light() +
  theme(legend.position = "bottom") +
  guides(col = guide_legend(nrow = 1))

Answer 1

I find this hybrid boxplot very, very lovely so I wanted to recreate it too.

I wrote a geom_boxjitter that inherits from geom_boxplot and only adds minor changes:

• It draws the geom_rect only on the left half.
• It jitters the points with default width of the right half, default height 0.4*resolution and can also take a seed argument.
• It adds additional whiskers (the horizontal ones) if errorbar.draw is set to TRUE. Their length can also be adjusted.

You can check the code here. I think it is great how easy it has become to alter existing geoms with slight changes. Using part of your data:

library(tidyverse)
library(cowplot)
library(ggparl)

P <- ggplot(
  dat_long %>% filter(key %in% c("p1", "p2")), 
  aes(x = type, y = value, fill = key)) +
  geom_boxjitter(outlier.color = NA, jitter.shape = 21, jitter.color = NA, 
                 jitter.height = 0.05, jitter.width = 0.075, errorbar.draw = TRUE) +
  theme(legend.position = "none") +
  ylim(c(-0.05, 1.05)) + 
  scale_fill_manual(values = c("#ecb21e", "#812e91"))
P