Reputation: 77
I don't know whether I have expressed myself correctly in the title, but I hope it is easy to understand when you see the following figures. For the start, this is my data:
hydrocarbons average SD type group
N 6,21 4,632774217 PAHs Naphtalenes
N1 4,71 2,43670665 PAHs Naphtalenes
N2 7,6 3,266286228 PAHs Naphtalenes
N3 16,18 11,00643289 PAHs Naphtalenes
N4 18,8 4,59631824 PAHs Naphtalenes
F 16,87 7,022165062 PAHs Fluorenes
F1 16,64 5,721267073 PAHs Fluorenes
F2 18,67 8,467132345 PAHs Fluorenes
F3 22,79 0,988021105 PAHs Fluorenes
P 7,97 0,211647391 PAHs Phenanthrenes
P1 26,66 16,64819987 PAHs Phenanthrenes
P2 21,72 4,416811664 PAHs Phenanthrenes
P3 18,99 4,635405486 PAHs Phenanthrenes
P4 66,28 7,706085861 PAHs Phenanthrenes
D 8,33 0,89862145 PAHs Dibenzothiophenes
D1 8,63 PAHs Dibenzothiophenes
D2 9,57 PAHs Dibenzothiophenes
D3 20,69 3,453922632 PAHs Dibenzothiophenes
D4 32,5 8,191613185 PAHs Dibenzothiophenes
FL 10,37 PAHs Fluoranthenes
PY 10,53 PAHs Fluoranthenes
FL1 24,42 8,886055918 PAHs Fluoranthenes
FL2 42,52 9,466539232 PAHs Fluoranthenes
FL3 51,99 15,77786373 PAHs Fluoranthenes
C 74,28 9,560499532 PAHs Chrysenes
C1 46,56 15,86163409 PAHs Chrysenes
C2 82,85 4,854714782 PAHs Chrysenes
C3 114,42 41,70884318 PAHs Chrysenes
nC-10 2,24 alkanes
nC-11 2,24 alkanes
nC-12 4,85 1,414267191 alkanes
nC-13 5,54 0,089306765 alkanes
nC-14 6,81 0,241222891 alkanes
nC-15 5,56 alkanes
nC-16 5,95 alkanes
nC-17 5,82 alkanes
nC-18 5,7 alkanes
nC-19 6,41 alkanes
nC-20 7,36 alkanes
nC-21 6,24 alkanes
nC-22 6,07 alkanes
nC-23 6,35 alkanes
nC-24 7,32 alkanes
nC-25 6,6 2,215395794 alkanes
nC-26 5,97 1,839829721 alkanes
nC-27 6,51 1,972060107 alkanes
nC-28 7,57 1,797509743 alkanes
nC-29 8,37 3,004883333 alkanes
nC-30 9,05 3,503601406 alkanes
nC-31 10,27 4,242811665 alkanes
nC-32 11,5 5,087821955 alkanes
nC-33 14,31 8,085948386 alkanes
nC-34 16,96 10,10105484 alkanes
nC-35 20,52 14,1878649 alkanes
nC-36 21,88 13,40071226 alkanes
n-C5 (Pentane) 10,63 1,715015757 VOCs
n-C6 (Hexane) 1,74 0,859880844 VOCs
n-C7 (Heptane) 9,62 4,316473516 VOCs
n-C9 (Nonane) 2,34 0,044641 VOCs
Benzene 23,51 0,631882255 VOCs
Toluene 18,48 2,369137637 VOCs
Ethylbenzene 7,55 7,171631537 VOCs
m-Xylene 12,53 7,250491275 VOCs
p-Xylene 15,21 1,800247445 VOCs
o-Xylene 21,96 2,184177383 VOCs
Propylbenzene 12,8 15,31136895 VOCs
n-Butylbenzene 9,33 5,486543125 VOCs
n-Pentylbenzene 6,77 0,420247353 VOCs
I want to plot half-lifes ("average") of my hydrocarbons and facet it according the "type". However, only for type "PAHs" I would like to have additional facet according the "group". The best I was able to code and plot is the following figure and it's not quite what I want :
This is the code I'm using:
all <- read.delim2("E#6-results_chemistry.txt", header=TRUE)
library(ggplot2)
all$hydrocarbons <- factor(all$hydrocarbons, levels = all$hydrocarbons) #keeps the order of x-axis same as in table
levels(all$type)[levels(all$type)=="alkanes"] <- "n-alkanes" #if needed to change specific labels in a column
ggplot(all, aes(x=hydrocarbons, y=average)) +
geom_bar(position = position_dodge(), stat="identity", fill="gray32") +
geom_errorbar(aes(ymin=average-SD, ymax=average+SD), color="gray8") +
facet_wrap(~type, scales="free", ncol=1) +
ylab("Half-life [d]") + xlab("Hydrocarbons") +
theme(axis.text.x=element_text(size=12, color="black", angle=45, hjust=1),
axis.title.x = element_text(size=14, face="bold", vjust=-0.7),
axis.title.y = element_text(size=14, face="bold", vjust=2),
axis.text.y = element_text(size=12, colour="black"))
Now, the question is, Is it possible to make a graphic where I would be able to make an additional facet strip, within existing one, only for "PAHs" type according to the "group"? The graphics would look something like this:
It would also work for me, if possible, to make a second x axis for "PAHs" which would arrange it according the "group".
Thanks, Deni
Upvotes: 4
Views: 301
Reputation: 32859
I think you will need to delve into the ggplot structure. This approach takes your original plot, but drops the middle panel (but keeps the space). I construct the middle panel as a separate plot, including the facets for the levels of 'PAHs'. I extract the relevant material (plot panel, strips, x-axis, and y-axis) from this plot to insert it into the empty spaces in the original plot. Then, I construct a new strip to contain the variable name 'PAHs'. The method ensures that the heights of the three panels are the same, unit(1, "null")
. (See below after the plot for the all
data frame that I used.)
Minor edit: Updating to ggplot2 2.2.1
library(ggplot2)
library(gtable)
library(grid)
all$hydrocarbons <- factor(all$hydrocarbons, levels = all$hydrocarbons) #keeps the order of x-axis same as in table
levels(all$type)[levels(all$type)=="alkanes"] <- "n-alkanes" #if needed to change specific labels in a column
# Original plot
pAll <- ggplot(all, aes(x = hydrocarbons, y = average)) +
geom_bar(position = position_dodge(), stat="identity", fill = "gray32") +
geom_errorbar(aes(ymin = average-SD, ymax = average+SD), color = "gray8") +
facet_wrap( ~ type, scales = "free", ncol = 1) +
ylab("Half-life [d]") + xlab("Hydrocarbons") +
theme(axis.text.x = element_text(size = 12, color = "black", angle = 45, hjust = 1),
axis.title.x = element_text(size = 14, face = "bold", vjust = -0.7),
axis.title.y = element_text(size = 14, face = "bold", vjust = 2),
axis.text.y = element_text(size = 12, colour = "black"))
# Middle plot, but with facets for 'PAHs'
pMid <- ggplot(subset(all, type == "PAHs"), aes(x = hydrocarbons, y = average)) +
geom_bar(position = position_dodge(), stat = "identity", fill = "gray32") +
geom_errorbar(aes(ymin = average - SD, ymax = average + SD), color = "gray8") +
facet_grid(. ~ group, scales = "free", space = "free") +
ylab("Half-life [d]") +
theme(axis.text.x = element_text(size = 12, color = "black", angle = 45, hjust = 1),
axis.title.x = element_text(size = 14, face = "bold", vjust = -0.7),
axis.title.y = element_text(size = 14, face = "bold", vjust = 2),
axis.text.y = element_text(size = 12, colour = "black"))
# Get the ggplot grobs
gAll <- ggplotGrob(pAll)
gMid <- ggplotGrob(pMid)
# In gMid, get the positions of the panels in the layout: t = top, l = left, ...
pos1 <- c(subset(gMid$layout, grepl("panel", gMid$layout$name), select = t:r))
# Extract 'panels' (along with x-axis and strips)
panels <- gMid[(unique(pos1$t) - 1) : (unique(pos1$t) + 1), min(pos1$l) : max(pos1$l)]
# Extract 'axisL' - y-axis
axisL <- gMid[unique(pos1$t), min(pos1$l) - 1]
# In gAll, get the positions of the panel of the middle plot in the layout
pos2 <- c(subset(gAll$layout, grepl("panel", gAll$layout$name), select = t:r))
pos2 <- lapply(pos2, "[", 2)
# Drop original panel material in the middle plot
drop <- gAll$layout$name %in% c("panel-1-2", "strip-t-1-2", "axis-b-1-2", "axis-l-2-1")
gAll$grobs[drop] <- NULL
gAll$layout <- gAll$layout[!drop,]
# Add new 'panels' to gAll
gAll <- gtable_add_grob(gAll, panels, t = pos2$t-1, l = pos2$l, b = pos2$t+1, name = "panels")
# Add new 'axisL' to gAll
gAll <- gtable_add_grob(gAll, axisL, t = pos2$t, l = pos2$l-1, name = "strips")
# Add row above the current strips
gAll <- gtable_add_rows(gAll, gAll$heights[pos2$t-1], pos2$t-2)
# Add grob, a new strip containing variable name 'PAHs', into the new row
gAll <- gtable_add_grob(gAll,
list(rectGrob(gp = gpar(col = NA, fill = "gray85")),
textGrob("PAHs", gp = gpar(fontsize = 9.6))),
t = pos2$t-1, l = pos2$l, name = c("background", "text"))
# Add a small gap between the strips
gAll <- gtable_add_rows(gAll, unit(1/10, "line"), pos2$t-1)
# Probably not needed, but if axisB font size in pMid is different from pAll
gAll$heights[pos2$t + 3] <- gMid$heights[unique(pos1$t) + 1]
# Draw it
grid.newpage()
grid.draw(gAll)
all = structure(list(hydrocarbons = structure(c(21L, 28L, 29L, 30L,
31L, 12L, 13L, 14L, 15L, 60L, 62L, 63L, 64L, 65L, 6L, 7L, 8L,
9L, 10L, 16L, 67L, 17L, 18L, 19L, 2L, 3L, 4L, 5L, 32L, 33L, 34L,
35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L,
48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L, 58L, 23L, 24L,
25L, 26L, 1L, 68L, 11L, 20L, 61L, 59L, 66L, 22L, 27L), .Label = c("Benzene",
"C", "C1", "C2", "C3", "D", "D1", "D2", "D3", "D4", "Ethylbenzene",
"F", "F1", "F2", "F3", "FL", "FL1", "FL2", "FL3", "m-Xylene",
"N", "n-Butylbenzene", "n-C5 (Pentane)", "n-C6 (Hexane)", "n-C7 (Heptane)",
"n-C9 (Nonane)", "n-Pentylbenzene", "N1", "N2", "N3", "N4", "nC-10",
"nC-11", "nC-12", "nC-13", "nC-14", "nC-15", "nC-16", "nC-17",
"nC-18", "nC-19", "nC-20", "nC-21", "nC-22", "nC-23", "nC-24",
"nC-25", "nC-26", "nC-27", "nC-28", "nC-29", "nC-30", "nC-31",
"nC-32", "nC-33", "nC-34", "nC-35", "nC-36", "o-Xylene", "P",
"p-Xylene", "P1", "P2", "P3", "P4", "Propylbenzene", "PY", "Toluene"
), class = "factor"), average = c(6.21, 4.71, 7.6, 16.18, 18.8,
16.87, 16.64, 18.67, 22.79, 7.97, 26.66, 21.72, 18.99, 66.28,
8.33, 8.63, 9.57, 20.69, 32.5, 10.37, 10.53, 24.42, 42.52, 51.99,
74.28, 46.56, 82.85, 114.42, 2.24, 2.24, 4.85, 5.54, 6.81, 5.56,
5.95, 5.82, 5.7, 6.41, 7.36, 6.24, 6.07, 6.35, 7.32, 6.6, 5.97,
6.51, 7.57, 8.37, 9.05, 10.27, 11.5, 14.31, 16.96, 20.52, 21.88,
10.63, 1.74, 9.62, 2.34, 23.51, 18.48, 7.55, 12.53, 15.21, 21.96,
12.8, 9.33, 6.77), SD = c(4.632774217, 2.43670665, 3.266286228,
11.00643289, 4.59631824, 7.022165062, 5.721267073, 8.467132345,
0.988021105, 0.211647391, 16.64819987, 4.416811664, 4.635405486,
7.706085861, 0.89862145, NA, NA, 3.453922632, 8.191613185, NA,
NA, 8.886055918, 9.466539232, 15.77786373, 9.560499532, 15.86163409,
4.854714782, 41.70884318, NA, NA, 1.414267191, 0.089306765, 0.241222891,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2.215395794, 1.839829721,
1.972060107, 1.797509743, 3.004883333, 3.503601406, 4.242811665,
5.087821955, 8.085948386, 10.10105484, 14.1878649, 13.40071226,
1.715015757, 0.859880844, 4.316473516, 0.044641, 0.631882255,
2.369137637, 7.171631537, 7.250491275, 1.800247445, 2.184177383,
15.31136895, 5.486543125, 0.420247353), type = structure(c(2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L), .Label = c("alkanes", "PAHs", "VOCs"), class = "factor"),
group = structure(c(6L, 6L, 6L, 6L, 6L, 5L, 5L, 5L, 5L, 7L,
7L, 7L, 7L, 7L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("",
"Chrysenes", "Dibenzothiophenes", "Fluoranthenes", "Fluorenes",
"Naphtalenes", "Phenanthrenes"), class = "factor")), .Names = c("hydrocarbons",
"average", "SD", "type", "group"), class = "data.frame", row.names = c(NA,
-68L))
Upvotes: 5