How to create 5x1 matrix geom_bar facet and allowing negative value in bar to go down y-axis in ggplot?

pdubois Published at Dev

pdubois

The following figure:

enter image description here

Was generated with the following code:

library(ggplot2)
library(reshape2)

dat <- structure(list(Type = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 
6L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L), .Label = c("High_expression", 
"KD.ip", "LG.ip", "LN.id", "LV.id", "LV.ip", "SP.id", "SP.ip"
), class = "factor"), ImmGen = structure(c(1L, 2L, 3L, 4L, 5L, 
6L, 7L, 8L, 9L, 10L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 
1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 1L, 2L, 3L, 4L, 5L, 
6L, 7L, 8L, 9L, 10L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L), .Label = c("Bcells", 
"DendriticCells", "Macrophages", "Monocytes", "NKCells", "Neutrophils", 
"StemCells", "StromalCells", "abTcells", "gdTCells"), class = "factor"), 
    Exp_06hr = c(7174.40482999999, 23058.74882, 39819.39133, 
    15846.46146, 8075.78226, 105239.11609, 7606.34563, 19513.57747, 
    7116.51211, 6978.64995, 498.36828, 732.01788, 621.51576, 
    546.63461, 529.1711, 545.17219, 477.54658, 1170.50303, 550.99528, 
    607.56707, 775.0691, 1269.50773, 2138.69883, 1561.74652, 
    601.9372, 5515.59896, 744.48716, 997.32859, 639.13126, 657.64581, 
    4165.29899, 5465.1883, 7773.25723, 5544.86758, 3461.13442, 
    8780.64899, 4380.00437, 8721.84871, 3674.62723, 3911.00108, 
    2932.76554, 5903.48407, 6179.81046, 3683.64539, 2744.59622, 
    6760.37307, 4097.14665, 6845.31988, 2872.77771, 2912.84262
    ), Exp_24hr = c(1596.9091, 4242.52354, 9984.68861, 3519.18627, 
    1602.92511, 12203.57109, 1656.19357, 3389.93866, 1617.35484, 
    1579.00309, 715.47289, 643.98371, 689.40412, 580.26036, 608.22853, 
    695.10737, 830.77947, 670.34899, 640.67908, 637.47464, 356.75713, 
    393.13449, 549.60095, 466.76064, 336.95453, 617.20976, 339.2476, 
    469.57407, 292.86365, 305.45178, 2604.07605, 4210.64843, 
    5797.13123, 3650.88447, 2275.03269, 6475.27485, 2604.70614, 
    4796.3314, 2411.09694, 2458.23237, 1498.21516, 1996.6875, 
    2927.82836, 1911.00463, 1523.57171, 2199.62297, 1541.82034, 
    2815.82184, 1608.46099, 1588.80561), ExpDiff_06_24hr = c(5577.49572999999, 
    18816.22528, 29834.70272, 12327.27519, 6472.85715, 93035.545, 
    5950.15206, 16123.63881, 5499.15727, 5399.64686, -217.10461, 
    88.03417, -67.88836, -33.62575, -79.05743, -149.93518, -353.23289, 
    500.15404, -89.6838, -29.9075700000001, 418.31197, 876.37324, 
    1589.09788, 1094.98588, 264.98267, 4898.3892, 405.23956, 
    527.75452, 346.26761, 352.19403, 1561.22294, 1254.53987, 
    1976.126, 1893.98311, 1186.10173, 2305.37414, 1775.29823, 
    3925.51731, 1263.53029, 1452.76871, 1434.55038, 3906.79657, 
    3251.9821, 1772.64076, 1221.02451, 4560.7501, 2555.32631, 
    4029.49804, 1264.31672, 1324.03701)), .Names = c("Type", 
"ImmGen", "Exp_06hr", "Exp_24hr", "ExpDiff_06_24hr"), row.names = c(NA, 
-50L), class = "data.frame")

dat.m <- melt(dat)

 setwd("~/Desktop/")
 pdf("myfig.pdf",width=30,height=20)
 p <- ggplot(dat.m,aes(ImmGen,value)) + 
 geom_bar(aes(fill = variable),position = "dodge",stat="identity")+
 facet_wrap(~Type) 

 p
 dev.off();

How can I modify it such that instead of wrapping it to (2x3) matrix like the above, we create (5x1) matrix instead. So each row will have its on scale of y-axis.

Secondly notice that the blue-bar (ExpDiff_06_24hr) can contain negative value. How can I show that so that in the plot the bar goes below 0 in y-axis.

Jaap

I think the subplots shouldn't be plotted in one row but in one column for clarity reasons. Whith some help of this answer (thanks to hrbrmstr for linking to it) and because I think this question deserves an answer, here is a solution:

dat$rank <- rank(dat$ExpDiff_06_24hr)
dat.m <- melt(dat, id = c("Type","ImmGen","rank"))

dat.t <- transform(dat.m, TyIm = factor(paste0(Type, ImmGen)))
dat.t <- transform(dat.t, TyIm = reorder(TyIm, rank(rank)))

p <- ggplot(dat.t, aes(TyIm,value)) + 
  geom_bar(aes(fill = variable), position = "dodge", stat="identity")+
  facet_wrap(~Type, ncol=1, scales="free") +
  scale_x_discrete("ImmGen", breaks=dat.t$TyIm, labels=dat.t$ImmGen)
p

The result: enter image description here

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edited at2021-03-14

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