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

Question

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.

changing the `facet_wrap()` call to `facet_wrap(~Type, nrow=1, scales="free")` should do what you want (including having the negative numbers go below the axis in the second facet). — hrbrmstr, Mar 17 '14 at 03:05
also +100 for the use of `dput()` to generate the code for the `data.frame` :-) — hrbrmstr, Mar 17 '14 at 03:06
@hrbrmstr: Thanks. Lastly, is there a way to sort the x-axis based on "ExpDiff_06_24hr" ? — pdubois, Mar 17 '14 at 03:10
just clarifying… you want the order of the bars in all the facets to be based on the values of `ExpDiff_06_24hr`, correct? — hrbrmstr, Mar 17 '14 at 03:19
if the answer to that clarification question is "yes", then you should be able to ref this SO answer http://stackoverflow.com/questions/5409776/how-to-order-bars-in-faceted-ggplot2-bar-chart to do the reordering. The use of the term 'hack' by those posters is most appropriate, too :-) — hrbrmstr, Mar 17 '14 at 03:21
The key is to order factor levels. For instance http://stackoverflow.com/questions/6867393/how-to-change-order-of-boxplots-when-using-ggplot2/6867418#6867418 or http://stackoverflow.com/questions/3622407/ordered-factors-in-ggplot2-bar-chart — Roman Luštrik, Mar 17 '14 at 07:21
About the `ExpDiff_06_24hr` variable: it seems like this variable is calculated by substracting `Exp_24hr` from `Exp_06hr` (which both look like certain points in time). Consequently an increase from `Exp_06hr` to `Exp_24hr` results in a negative difference. Shouldn't it be the other way around? — Jaap, Mar 17 '14 at 21:27

score 1 · Accepted Answer · edited May 23 '17 at 11:43

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

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

1 Answers1