I want to enlarge the size of the axis labeling.
par(mar=c(1,1,1,1))
scatter3D(x = Eplot_sand.mean$OM, y = Eplot_sand.mean$rho_B, z = Eplot_sand.mean$Pv.mean,
phi = 20, theta = 35, bty = "b2", type = "h",alpha = 0.8, clim =c(0,150),
ticktype = "detailed", pch = 19, cex = 1.2, clab = "Pv (kPa)",
xlab = "OM (%)",
revolutions=100,
zlab = "Pv (kPa)",
ylab = "bulk density (g cm-³)",
bg.col="black",
sphere.size=100,
xlim = c(0,5),
ylim = c(1,2),
zlim = c(0,150),
col = ramp.col(c("blue", "green","orange", "red")))
Thanks in advance!
Similarly to the limit command in your function (xlim etc), you can do a cex command for your label indicating the size of text be scaled relative to the default:
scatter3D(...,
cex.lab=par("cex.lab"))
This is also slightly documented here:
https://www.rdocumentation.org/packages/scatterplot3d/versions/0.3-41/topics/scatterplot3d
Related
I want to make a scatter 3D Plot with PC_1 and PC_3 (subscripts) as labels of the x- and z-axis. I would usually do it with expression(PC[1]) but it doesn't work. I just can't find a way to solve the problem.
library(plot3D)
par(mar = c(4, 0, 3.2, 2))
scatter3D(pc$PC1, pc$PC2, pc$PC3, phi = phi, theta = 180,
colvar = as.integer(sz$t)/60, clab = c("Zeit in", "Minuten"),
col = ramp.col(c("deepskyblue", "blue", "darkorchid", "violetred", "red")),
bty = "b2", type = "b", ticktype = "detailed",
pch = 20, lwd = 2, cex.lab = 1.4, cex.axis = 1.4, cex = 1,
colkey = FALSE, main = "",
xlab = expression(PC[1]), ylab = "", zlab = expression(PC[3]),
xlim = c(min(pc), max(pc)), ylim = c(min(pc), max(pc)), zlim = c(min(pc), max(pc))
)
It just shows PC[1] and PC[3] as axis labels. PC["1"] and "PC"["1"] or any other combination also don't work.
I want to plot in R several panels with data measured along a sediment core (see image below). Next to the plots, I want to add a photo of that sediment core, aligned to the exact y coordinates as the plots (to be able to identify if a certain layer in the photo corresponds to a peak in some element in the plot).
The piece of code below produces de multipanel plot plus the photo (see below as well). As you can see using the tape measure in the photo, the y coordinates of the plots do not match the coordinates of the photo.
op <- par(mfrow = c(1,4), oma = c(5,4,2,0) + 0.1, mar = c(0,0,4,1) + 0.1, pch = 20)
plot(y = -curian3_scores$Sample, x = curian3_scores$RC1, xaxt = "n", type = "o", pch =16, ylab = "", xlab = "", lwd = 1.5, col = "blue", ylim = c(-1197.744, -40), cex.axis = 1.2)
axis(3, cex.axis = 1.2)
mtext(side = 3, text = var.PC1, line = 2.2, cex = 0.9)
mtext(side = 2, text = "Depth (mm)", line = 3, cex = 0.9)
plot(y = -curian3_scores$Sample, x = curian3_scores$RC2, xaxt = "n", yaxt = "n", type = "o", ylab = "", xlab = "", lwd = 1.5, col = "red", ylim = c(-1197.744, -40), cex.axis = 1.2)
axis(3, cex.axis = 1.2)
mtext(side = 3, text = var.PC2, line = 2.2, cex = 0.9)
plot(y = -curian3_scores$Sample, x = curian3_scores$RC3, xaxt = "n", yaxt = "n", type = "o", ylab = "", xlab = "", lwd = 1.5, col = "darkgreen", ylim = c(-1197.744, -40), cex.axis = 1.2)
axis(3, cex.axis = 1.2)
mtext(side = 3, text = var.PC3, line = 2.2, cex = 0.9)
# Charge the image as an R object with the "JPEG" package
library(jpeg)
my_image=readJPEG("~/Documents/FEINA/POSTDOCTORAT/RESILCOAST/ARTICLES/Carbon_persistence/Data_mining/CoreScanner/Core_Images_for_R/CURIAN3a_8.jpg")
# Set up a plot area with no plot
plot(y = -curian3_scores$Sample, x = curian3_scores$RC3, type = "n", axes = F, ylab = "", xlab = "")
# Get the plot information so the image will fill the plot box, and draw it
lim <- par()
rasterImage(my_image, xleft = lim$usr[1], ybottom = lim$usr[3], xright = lim$usr[2], ytop = lim$usr[4])
par(op)
Any ideas to make the photo's and plots' coordinates to match? If the ylim in each plot worked, I think this would be it... however, I think they're overruled for some reason...
For a customer I'm trying to do a combined barplot and lineplot (with points) with two y axis.
Problem: My bars and points are not aligned.
Background: We have several machines and are measuring their number of on/of switches and the amount of time that each machine is running. We want both information together in one plot to save space, because we have several machines.
The data is aggregated by day or hour. Here's some sample data:
date <- seq(as.Date("2016-10-01"), as.Date("2016-10-10"), "day")
counts <- c(390, 377, 444, NA, NA, NA, NA, 162, 166, 145)
runtime <- c(56.8, 59.4, 51.0, NA, NA, NA, NA, 38.5, 40.9, 43.4)
df <- data.frame(date = date, counts = counts, runtime = runtime)
Here's what I tried so far:
par(mar = c(3,4,4,4) + 0.3)
barplot(df$runtime, col = "palegreen2", border = "NA", ylab = "runtime in [%]",
ylim = c(0,100), font.lab = 2)
par(new = TRUE)
ymax <- max(df$counts, na.rm = TRUE) * 1.05
plot(df$date, df$counts, type = "n", xlab = "", ylab = "", yaxt = "n",
main = "Machine 1", ylim = c(0, ymax))
abline(v = date, col = "red", lwd = 2.5)
lines(df$date, df$counts, col = "blue", lwd = 2)
points(df$date, df$counts, pch = 19, cex = 1.5)
axis(4)
mtext("Number of switching operations", side = 4, line = 3, font = 2)
I found some inspiration for two axis here: http://robjhyndman.com/hyndsight/r-graph-with-two-y-axes/
What can I do to get bars with their middle aligned with the points of the lineplot?
The problem you are running into is the call to the second plot function after the barplot. This is shifting/resizing the plotting canvas which is causing the shift in the subsequent points.
Here is a quick work-around that just rescales the points and lines onto the barplot. It saves the barplot as an object, which stores x-axis locations for the mid-points of the bars. Then, when you plot the abline, lines and points using 'bp' as the x-axis variable, they will be correctly aligned.
ymax <- max(df$counts, na.rm = TRUE) * 1.05
par(mar=c(4.1,5.1,2.1,5.1))
bp <- barplot(df$runtime, col = "palegreen2", border = "NA", ylab = "runtime in [%]",
ylim = c(0,100), font.lab = 2, xlim=c(0.2,12), )
barplot(df$runtime, col = "palegreen2", ylab = "runtime in [%]", border="NA",
ylim = c(0,100), font.lab = 2)
abline(v = bp, col = "red", lwd = 2.5)
lines(bp, df$counts/ymax*100, col = "blue", lwd = 2)
points(bp, df$counts/ymax*100, pch = 19, cex = 1.5)
axis(4,at=c(0,20,40,60,80,100), labels=c("0","100","200","300","400","500"))
mtext("Number of switching operations", side = 4, line = 3, font = 2)
axis(1, at=bp, labels=df$date)
#emilliman: Thank you for your patience and input! Your plot is not completely correct, because the scaling of the second y-axis does not fit the points' values, but your idea helped me to find a solution!
Here's my new code:
library(plyr)
ymax <- max(df$counts, na.rm = TRUE)
ymax_up <- round_any(ymax, 100, f = ceiling)
ylab <- ymax_up/5 * c(0:5)
par(mar = c(3,4,4,4) + 0.3)
bp <- barplot(df$runtime, col = "palegreen2", border = "NA", ylab = "runtime in [%]",
ylim = c(0,100), font.lab = 2, main = "Machine 1")
abline(v = bp, col = "red", lwd = 2.5)
lines(bp, 100/ymax_up * df$counts, col = "blue", lwd = 2)
points(bp, 100/ymax_up * df$counts, pch = 19, cex = 1.5)
axis(4,at=c(0,20,40,60,80,100), labels= as.character(ylab))
mtext("Number of switching operations", side = 4, line = 3, font = 2)
xlab <- as.character(df$date, format = "%b %d")
axis(1, at=bp, labels = xlab)
abline(h = c(0,100))
(http://i.imgur.com/9YtYGSD.png)
Maybe this is helpful for others who run into this problem.
I know this type of question has been posted several times, but I tried all different suggestions and nothing works for me. I would like to have the x-axis labels on my bar plot positioned at 45 degrees. My code at the moment is like this:
barplot(t(all.vac_models01[1:28,3:4]), ylab = expression("Proportion of "*italic("R"^"2")),
las=2, cex.names = 0.9,
legend.text = gsub("prop_attributed_to_visit", "Intraindividual",
gsub(pattern = "prop_attributed_to_patientID",
replacement = "Interindividual", colnames(all.vac_models01[1:28,3:4]))),
args.legend = list(x= 30, y = 1.3, xpd = T, horiz = T, bg = "white", bty ="o", box.lwd = 0))>
Try this:
x <- barplot(t(all.vac_models01[1:28,3:4]), ylab = expression("Proportion of "*italic("R"^"2")),
las=2, cex.names = 0.9,
legend.text = gsub("prop_attributed_to_visit", "Intraindividual",
gsub(pattern = "prop_attributed_to_patientID",
replacement = "Interindividual", colnames(all.vac_models01[1:28,3:4]))),
args.legend = list(x= 30, y = 1.3, xpd = T, horiz = T, bg = "white", bty ="o", box.lwd = 0),
xaxt="n")
labs <- names(t(all.vac_models01[1:28,3:4]))
text(cex=1, x=x, y=-1.25, labs, xpd=TRUE, srt=45, pos=2)
Assigning the barplot call to x allows you to store the position of the labels. Be sure to specify xaxt="n" so that the labels are not printed initially.
I'm plotting a cdf of some data, and I've added logarithmic scale on the "x" axis.
The ticks spacing is exactly as I want it to be, but I'd like to be able to add
some tick marks on specific points.
I don't want to change the distribution of the ticks in my plot, from n by n to m by m, I want simply to have, among the ticks from n by n, some further tick marks on some values.
I'd like to have it reflected in both x and y axis, so that I can fit a grid into these new marks throughout the graph.
So far I have the graph, and the grid -- I don't mind about having the grid behind or upon the graph, I just want to add some custom ticks.
# Cumulative Distribuition
pdf("g1_3.pdf")
plot(x = f$V2, y = cumsum(f$V1), log = "x", pch = 3,
xlab = "Frequency", ylab = "P(X <= x)",
panel.first = grid(equilogs = FALSE))
axis(1, at = c(40, 150))
abline(h = 0.6, v = 40, col = "lightgray", lty = 3)
abline(h = 0.6, v = 150, col = "lightgray", lty = 3)
dev.off()
UPDATE: The graph I have so far:
Considering the initial script, and the tips given by #BenBolker, I had to use:
axis(side = 1, at = c([all the ticks you want]))
in order to add the ticks in the graph. Here's the final result:
# Cumulative Distribuition
pdf("g1_3.pdf")
plot(x = f$V2, y = cumsum(f$V1), log = "x", pch = 3,
xlab = "Frequency", ylab = "P(X <= x)", axes = FALSE)
ticks = c(1, 5, 10, 40, 150, 500, 1000)
axis(side = 1, at = ticks)
axis(side = 2)
abline(h = seq(0, 1, 0.2), v = ticks, col = "lightgray", lty = 3)
box()