I am trying to rotate one of the labels on my grid.arrange panel figure to look like the axis of all three plots, but this is not working using the methods I am finding online.
When I use a textGrob for control of the font size (which I need to be 24), using this code, I get this figure. I am inserting the rot= 90 argument but it isn't doing anything to the figure.
grid.arrange(d.a.plot1, d.b.plot1, d.c.plot1, ncol = 1, left = textGrob("Probability of remaining availabile", gp=gpar(fontsize=24, rot = 90)), bottom = textGrob("Depth(cm)", gp=gpar(fontsize = 24)))
When I use the standard grid.arrange code to add a rotated label using the code below, the position is fine, but then I can't adjust the font.
grid.arrange(d.a.plot1, d.b.plot1, d.c.plot1, ncol = 1, left = "Probability of remaining availabile", bottom = textGrob("Depth(cm)", gp=gpar(fontsize = 24)))
You just need to take rot = 90 out of gpar and pass it directly to textGrob:
# Simulate the plot grobs:
f <- function() cowplot::as_grob(~plot(rnorm(100), rnorm(100)))
grid.arrange(f(), f(), f(), ncol = 1,
left = textGrob("Probability of remaining availabile", rot = 90,
gp = gpar(fontsize=24)),
bottom = textGrob("Depth(cm)", gp=gpar(fontsize = 24)))
Related
So I've been trying to stitch a set of four plots together and the bottom right x-axis always gets covered with axis title. Originally I thought it might have been because the bottom right plot had a slightly larger y-axis but it doesn't matter which graph I stick in the bottom right corner it always gets covered up....
Here is my code:
tiff('Predictors.tiff', units = "in", width = 12, height = 12, res = 1200)
ggarrange(PC5,PN5,HW5,CN5, ncol = 2, nrow = 2)
annotate_figure(figure,top = text_grob("Predictors of N Mineralization", size = 20),
left = text_grob("N mineralization after 6 months (mg/kg)", size = 20, rot = 90))
dev.off()
PC5,PN5 etc. are all names of plots
I had trouble trying to remove the vertical white space between each plot. I have several plots so I used ggarrange to combine them.
This is my code:
figure <- ggarrange(lima_exceso,loreto_exceso,amazonas_exceso,madre_exceso,
callao_exceso,apurimac_exceso,ancash_exceso,
sanmartin_exceso, ica_exceso,ayacucho_exceso,
arequipa_exceso, piura_exceso,junin_exceso,pasco_exceso,
cusco_exceso,lambayeque_exceso,huancavelica_exceso,
puno_exceso,tumbes_exceso,lalibertad_exceso,
tacna_exceso,huanuco_exceso,cajamarca_exceso,
labels = c(""),
ncol = 4, nrow = 6)
annotate_figure(figure,
top = text_grob("Exceso de fallecidos (media móvil-7d)",
color = "black", face = "bold", size = 12),
bottom = text_grob("Data source: \n Minsa ",
color = "black", hjust = 0, x = 0, face = "italic",
size = 8), fig.lab = "", fig.lab.face = "bold",
fig.lab.pos = "top.right" , fig.lab.size = 8)
ggsave(file="ex31.pdf" , height = 350, units = "mm" , width = 340)
This is the outcome:
As you can see there is a lot of vertical space between the graphics and that's why the title is too close from the plots. The margin of the pdf is tiny.
So I tried to narrow that space by setting margins for each plot (just for the first column), however, the outcome was not what I wanted.
I add this line code to the plots of the first column:
+theme(plot.margin = unit(c(-0.25,0.5,-0.25,0.5), "lines"))
This was the outcome:
As you can see I narrowed the vertical space but now the plots of the first column are taller than the others, and the title of the first plot (right corner) is too close from the ggarrange title. I want to reduce the space between the plots but I don't want to modify anything else.
Is there a way to reduce the vertical space of my plots using ggarrange?
I use the following script to generate a legend in R. But the legend box is too small... how do I increase the box width?
legend("topleft", lty = 1, legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),col = c("black","red","blue"))
You are probably resizing your graph after you plot it and the legend. If that is the case, and you want to keep the box, one option would be to plot the graph, resize it, and then generate the legend. Perhaps a better option would be to size the window to the desired width to start with:
# on Windows, you can use the `windows` function. elsewhere, try quartz or X11
windows(height = 7, width = 3.5)
plot(hp ~ mpg, data = mtcars)
leg <- legend("topleft", lty = 1,
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"),
#plot = FALSE,
#bty = "n")
)
You can also define exactly where you want the box to fall by providing a pair of x and y coordinates to the legend function. Those values would represent the upper left and bottom right corners of the box. The legend function will actually generate the coordinates for the upper-left hand corner of the box along with the width and height. By default it returns them invisibly, but you can assign them to an object, and If you use the plot = FALSE, option to legend you can capture those coordinates and modify them as you wish without actually plotting the legend.
windows(height = 7, width = 3.5)
plot(hp ~ mpg, data = mtcars)
legend(x = c(9.46, 31), y = c(346.32, 298),
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"),
lty = 1)
The legend function will actually generate the coordinates for the upper-left hand corner of the box (that's where I got 9.46 and 346.62) along with the width and height of the box. By default it returns them invisibly, but you can assign them to an object, and if you use the plot = FALSE, option to legend you can capture those coordinates and modify them as you wish without actually plotting the legend.
plot(hp ~ mpg, data = mtcars)
leg <- legend("topleft", lty = 1,
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"),
plot = FALSE)
# adjust as desired
leftx <- leg$rect$left
rightx <- (leg$rect$left + leg$rect$w) * 1.2
topy <- leg$rect$top
bottomy <- (leg$rect$top - leg$rect$h) * 1
# use the new coordinates to define custom
legend(x = c(leftx, rightx), y = c(topy, bottomy), lty = 1,
legend = c("Sub_metering_1","Sub_metering_2","Sub_metering_3"),
col = c("black","red","blue"))
Part of the legend width is determined by the longest width of the labels you use, which is calculated via strwidth. Below an easy example how to halve or double the size by using legend(..., text.width = ...).
plot(1)
text = c("Sub_metering_1","Sub_metering_2","Sub_metering_3")
legend("topleft"
,lty = 1
,legend = text
,col = c("black","red","blue")
)
strwidth(text)
# [1] 0.1734099 0.1734099 0.1734099
# half the length
legend("bottomleft"
,lty = 1
,legend = text
,text.width = strwidth(text)[1]/2
,col = c("black","red","blue")
)
# double the length
legend("center"
,lty = 1
,legend = text
,text.width = strwidth(text)[1]*2
,col = c("black","red","blue")
)
I'm using lsmip from lsmeans to plot my model,
library(lsmeans)
PhWs1 <- lsmip(GausNugget1, Photoperiod:Ws ~ Month,
ylab = "Observed log(number of leaves)", xlab = "Month",
main = "Interaction between Photoperiod and Water stress over the months (3 photoperiods)",
par.settings = list(fontsize = list(text = 15, points = 10)))
but I was not able to get a suggestion on the internet on how to handle the legend position, size, title, etc.
I used trellis.par.get() to see the parameters but I could not find the one related to my issue. As you can see from the graph, the legend should be "Photoperiod*Ws" but Ws is not visible.
I see two possibly complementing alternatives to approach this issue. The first would be to create a fully customized legend and pass it on to the key argument of xyplot (which lsmip is heavily based on). Here is an example taken from ?lsmip to clarify my point.
## default trellis point theme
trellis_points <- trellis.par.get("superpose.symbol")
## create customized key
key <- list(title = "Some legend title", # legend title
cex.title = 1.2,
x = .7, y = .9, # legend position
points = list(col = trellis_points$col[1:2], # points
pch = trellis_points$pch[1:2],
cex = 1.5),
text = list(c("A", "B"), cex = .9)) # text
## create results and extract lattice plot
d <- lsmip(warp.lm, wool ~ tension, plotit = FALSE,
main = "Some figure title", key = key)
p <- attr(d, "lattice")
p
As you can see, setting up a customized legend let's you modify all the different components of the legend - including labels, text and symbol sizes, legend spacing, etc. Have a deeper look at the key argument described in ?xyplot which describes the various modification options in detail.
Now, if you have a long legend title and you do not want to include the legend inside the plot area, you could also define separate viewports, thus allowing the legend to occupy more space at the right margin. Note the use of update to remove the initially created legend from p and the subsequent assembly of the single figure components using grid functionality.
## remove legend from figure
p <- update(p, legend = NULL)
## assemble figure incl. legend
library(grid)
png("plot.png", width = 14, height = 10, units = "cm", res = 300)
grid.newpage()
## add figure without legend
vp0 <- viewport(x = 0, y = 0, width = .75, height = 1,
just = c("left", "bottom"))
pushViewport(vp0)
print(p, newpage = FALSE)
## add legend
upViewport(0)
vp1 <- viewport(x = .7, y = 0, width = .3, height = 1,
just = c("left", "bottom"))
pushViewport(vp1)
draw.key(key, draw = TRUE)
dev.off()
I'm using the code below to generate the following chart.
# Setup
data(airquality)
# Device start
png(filename = "example.png", units = "cm", width = 20, height = 14, res = 300)
# Define chart
pairs.chrt <- ggpairs(airquality,
lower = list(continuous = "smooth"),
diag = list(continuous = "blank"),
upper = list(continuous = "blank")) +
theme(legend.position = "none",
panel.grid.major = element_blank(),
axis.ticks = element_blank(),
axis.title.x = element_text(angle = 180, vjust = 1, color = "black"),
panel.border = element_rect(fill = NA))
# Device off and print
print(pairs.chrt)
dev.off()
I'm currently trying to modify the display of the axis titles. In particular, I would like for the axis titles to be:
Placed at a further distance from axis labels
Placed at an angle
As an example, I would like to obtain axis titles similar to the ones pictured below (I'm interested in axis labels only, not in rest of the chart):
Taken from : Geovisualist
I' tried adjusting my syntax changing the axis.title.x to different values but it does not yield the desired results. For instance running the code with angle = 45.
axis.title.x = element_text(angle = 45, vjust = 1, color = "black"),
panel.border = element_rect(fill = NA))
returns the same chart. I was able to control the axis labels by changing the axis.text.x for instance but I can't find the answer how to control the axis titles in this plot. Any help will be much appreciated.
Short answer: There doesn't seem to be an elegant or easy way to do it, but here's a workaround.
I dug into the ggpairs source code (in the GGally package source available from CRAN) to see how the variable labels are actually drawn. The relevant function in ggpairs.R is print.ggpairs. It turns out the variable labels aren't part of the ggplot objects in each cell of the plot matrix -- i.e. they're not axis titles, which is why they aren't affected by using theme(axis.title.x = element_text(angle = 45) or similar.
Rather, they seem to be drawn as text annotations using grid.text (in package 'grid'). grid.text takes arguments including x, y, hjust, vjust, rot (where rot is angle of rotation), as well as font size, font family, etc. using gpar (see ?grid.text), but it looks like there is currently no way to pass in different values of those parameters to print.ggpairs -- they're fixed at default values.
You can work around it by leaving your variable labels blank to begin with, and then adding them on later with customized placement, rotation, and styling, using a modification of the relevant part of the print.ggpairs code. I came up with the following modification. (Incidentally, because the original GGally source code was released under a GPL-3 license, so is this modification.)
customize.labels <- function(
plotObj,
varLabels = NULL, #vector of variable labels
titleLabel = NULL, #string for title
leftWidthProportion = 0.2, #if you changed these from default...
bottomHeightProportion = 0.1, #when calling print(plotObj),...
spacingProportion = 0.03, #then change them the same way here so labels will line up with plot matrix.
left.opts = NULL, #see pattern in left.opts.default
bottom.opts = NULL, #see pattern in bottom.opts.default
title.opts = NULL) { #see pattern in title.opts.default
require('grid')
vplayout <- function(x, y) {
viewport(layout.pos.row = x, layout.pos.col = y)
}
numCol <- length(plotObj$columns)
if (is.null(varLabels)) {
varLabels <- colnames(plotObj$data)
#default to using the column names of the data
} else if (length(varLabels) != numCol){
stop('Length of varLabels must be equal to the number of columns')
}
#set defaults for left margin label style
left.opts.default <- list(x=0,
y=0.5,
rot=90,
just=c('centre', 'centre'), #first gives horizontal justification, second gives vertical
gp=list(fontsize=get.gpar('fontsize')))
#set defaults for bottom margin label style
bottom.opts.default <- list(x=0,
y=0.5,
rot=0,
just=c('centre', 'centre'),#first gives horizontal justification, second gives vertical
gp=list(fontsize=get.gpar('fontsize')))
#set defaults for title text style
title.opts.default <- list(x = 0.5,
y = 1,
just = c(.5,1),
gp=list(fontsize=15))
#if opts not provided, go with defaults
if (is.null(left.opts)) {
left.opts <- left.opts.default
} else{
not.given <- names(left.opts.default)[!names(left.opts.default) %in%
names(left.opts)]
if (length(not.given)>0){
left.opts[not.given] <- left.opts.default[not.given]
}
}
if (is.null(bottom.opts)) {
bottom.opts <- bottom.opts.default
} else{
not.given <- names(bottom.opts.default)[!names(bottom.opts.default) %in%
names(bottom.opts)]
if (length(not.given)>0){
bottom.opts[not.given] <- bottom.opts.default[not.given]
}
}
if (is.null(title.opts)) {
title.opts <- title.opts.default
} else{
not.given <- names(title.opts.default)[!names(title.opts.default) %in%
names(title.opts)]
if (length(not.given)>0){
title.opts[not.given] <- title.opts.default[not.given]
}
}
showLabels <- TRUE
viewPortWidths <- c(leftWidthProportion,
1,
rep(c(spacingProportion,1),
numCol - 1))
viewPortHeights <- c(rep(c(1,
spacingProportion),
numCol - 1),
1,
bottomHeightProportion)
viewPortCount <- length(viewPortWidths)
if(!is.null(titleLabel)){
pushViewport(viewport(height = unit(1,"npc") - unit(.4,"lines")))
do.call('grid.text', c(title.opts[names(title.opts)!='gp'],
list(label=titleLabel,
gp=do.call('gpar',
title.opts[['gp']]))))
popViewport()
}
# viewport for Left Names
pushViewport(viewport(width=unit(1, "npc") - unit(2,"lines"),
height=unit(1, "npc") - unit(3, "lines")))
## new for axis spacingProportion
pushViewport(viewport(layout = grid.layout(
viewPortCount, viewPortCount,
widths = viewPortWidths, heights = viewPortHeights
)))
# Left Side
for(i in 1:numCol){
do.call('grid.text',
c(left.opts[names(left.opts)!='gp'],
list(label=varLabels[i],
vp = vplayout(as.numeric(i) * 2 - 1 ,1),
gp=do.call('gpar',
left.opts[['gp']]))))
}
popViewport()# layout
popViewport()# spacing
# viewport for Bottom Names
pushViewport(viewport(width=unit(1, "npc") - unit(3,"lines"),
height=unit(1, "npc") - unit(2, "lines")))
## new for axis spacing
pushViewport(viewport(layout = grid.layout(
viewPortCount, viewPortCount,
widths = viewPortWidths, heights = viewPortHeights)))
# Bottom Side
for(i in 1:numCol){
do.call('grid.text',
c(bottom.opts[names(bottom.opts)!='gp'],
list(label=varLabels[i],
vp = vplayout(2*numCol, 2*i),
gp=do.call('gpar',
bottom.opts[['gp']]))))
}
popViewport() #layout
popViewport() #spacing
}
And here's an example of calling that function:
require('data.table')
require('GGally')
require('grid')
fake.data <- data.table(test.1=rnorm(50), #make some fake data for demonstration
test.2=rnorm(50),
test.3=rnorm(50),
test.4=rnorm(50))
g <- ggpairs(data=fake.data,
columnLabels=rep('', ncol(fake.data)))
#Set columnLabels to a vector of blank column labels
#so that original variable labels will be blank.
print(g)
customize.labels(plotObj=g,
titleLabel = 'Test plot', #string for title
left.opts = list(x=-0.5, #moves farther to the left, away from vertical axis
y=0.5, #centered with respect to vertical axis
just=c('center', 'center'),
rot=90,
gp=list(col='red',
fontface='italic',
fontsize=12)),
bottom.opts = list(x=0.5,
y=0,
rot=45, #angle the text at 45 degrees
just=c('center', 'top'),
gp=list(col='red',
fontface='bold',
fontsize=10)),
title.opts = list(gp=list(col='green',
fontface='bold.italic'))
)
(This makes some very ugly labels -- for the purposes of demonstration only!)
I didn't tinker with placing the labels somewhere other than the left and bottom -- as in your Geovisualist example -- but I think you'd do it by changing the arguments to vplayout in the "Left Side" and "Bottom Side" pieces of code in customize.labels. The x and y coordinates in grid.text are defined relative to a viewport, which divides the display area into a grid in
pushViewport(viewport(layout = grid.layout(
viewPortCount, viewPortCount,
widths = viewPortWidths, heights = viewPortHeights
)))
The call to vplayout specifies which cell of the grid is being used to position each label.
Caveat: not a complete answer but perhaps suggests a way to approach it. You can do this by editing the grid objects.
# Plot in current window
# use left to add space at y axis and bottom for below xaxis
# see ?print.ggpairs
print(pairs.chrt, left = 1, bottom = 1)
# Get list of grobs in current window and extract the axis labels
# note if you add a title this will add another text grob,
# so you will need to tweak this so not to extract it
g <- grid.ls(print=FALSE)
idx <- g$name[grep("text", g$name)]
# Rotate yaxis labels
# change the rot value to the angle you want
for(i in idx[1:6]) {
grid.edit(gPath(i), rot=0, hjust=0.25, gp = gpar(col="red"))
}
# Remove extra ones if you want
n <- ncol(airquality)
lapply(idx[c(1, 2*n)], grid.remove)
My answer won't fix the diagonal label issue but it will fix the overlay one.
I had this issue with the report I am currently writing, where the axis titles were always over the axes, especially in ggpairs. I used a combination of adjusting the out.height/out.width in conjunction with fig.height/fig.width. Separately the problem was not fixed, but together it was. fig.height/fig.width took the labels away from the axis but made them too small to read, and out.height/out.width just made the plot bigger with the problem unchanged. The below gave me the results shown:
out.height="400px", out.width="400px",fig.height=10,fig.width=10
before:plot with issues
after: