My layout doesn't allow me to show xlab and ylab - r

Question

It looks like something simple I am missing but have no idea how to deal with this.
So I used a layout() function and I managed to get the layout as I wanted as below picture. Iris data was used in my coding.
Problem is, it does not show me the x label and y label on the output when I use plot() functions after this. And xaxis and yaxis for plot() looks overlapping. I am not sure how to deal with this problem.
There was no problem for x and y labelling before introducing plot.new() and par() to set up the main name of my diagram. (i.e. before I use the code from plot.new() to title(), xlab and ylab were shown)
I used 6 different plots in my original code, including, the plot.new() for title(), but I omitted the rest of them for convenience
Here is my code below,
x <- iris$Sepal.Length
y <- iris$Species
x_min <- min(iris$Sepal.Length)
x_max <- max(iris$Sepal.Length)
y_min <- min(iris$Sepal.Width)
y_max <- max(iris$Sepal.Width)
layout(matrix(c(1,1,1,1,1,1,
2,2,3,3,4,4,
5,5,5,6,6,6), nc=6, byrow = TRUE), heights=c(lcm(1),1,1,1,1))
layout.show(6)
par("mar"=c(1,1,1,1,1,1))
plot.new()
plot.window(xlim=c(0,1), ylim=c(0,1))
text(x=0.5,y=0.5,"scatter and density plots for Sepal and Length and Sepal Width" ,font=2, cex=1.5)
plot(...)

Answer 1

You can use the xlab and ylab arguments in title. However, the way you have constructed the plot means that when you reset par at the end, these are drawn off the page due ti their position relative to your custom axis. If you simply leave par alone, you get:
den1 = density(CDE1$V1)
den2 = density(CDE1$V2)
col1 = hsv(h = 0.65, s = 0.6, v = 0.8, alpha = 0.5)
col2 = hsv(h = 0.85, s = 0.6, v = 0.8, alpha = 0.5)
plot.new()
plot.window(xlim = c(25,65), ylim = c(0, 0.14))
axis(side = 1, pos = 0, at = seq(from = 25, to = 65, by = 5), col = "gray20",
lwd.ticks = 0.25, cex.axis = 1, col.axis = "gray20", lwd = 1.5)
axis(side = 2, pos = 25, at = seq(from = 0, to = 0.14, by = 0.02),
col = "gray20", las = 2, lwd.ticks = 0.5, cex.axis = 1,
col.axis = "gray20", lwd = 1.5)
polygon(den1$x, den1$y, col = col1, border ="black",lwd = 2)
polygon(den2$x, den2$y, col = col2, border ="black",lwd = 2)
text(52, 0.10, labels ="CDET", col =col1, cex = 1.25,font=2)
text(35, 0.03, labels ="SDFT", col =col2, cex = 1.25,font=2)
title(main = "Gestational Day 100/283",
xlab = "Fibril Diameter (nm)",
ylab = "density")
Of course, you could get a similar plot with less code and much easier adjustments using ggplot:
library(ggplot2)
ggplot(tidyr::pivot_longer(CDE1, 1:2), aes(value, fill = name)) +
geom_density() +
scale_fill_manual(values = c(col1, col2), labels = c("CDET", "SDFT")) +
scale_x_continuous(breaks = seq(25, 65, 5), limits = c(25, 65)) +
scale_y_continuous(breaks = seq(0, 0.14, 0.02), limits = c(0, 0.14)) +
theme_classic(base_size = 16) +
labs(title = "Gestational Day 100/283", x = "Fibril Diameter (nm)",
fill = NULL) +
theme(plot.title = element_text(hjust = 0.5))
Data used
Obviously, we don't have your data, so I had to create a reproducible approximation:
set.seed(123)
CDE1 <- data.frame(V1 = rnorm(20, 47.5, 4), V2 = rnorm(20, 44, 5))