Plot with inwards ticks - base R

Plot inwards ticks - base R.R

# ==========================================================================
# Example of plot for publication in base R with inwards ticks
# ==========================================================================

# ==================================
# create some data
# ==================================
set.seed(1)
DF <- data.frame(year = c(2000:2020),
                 mean = rnorm(n=21, mean=100, sd=10))

# ==================================
# helper functions
# ==================================
# _____ Function to convert from given cm to lines of text
cm2line <- function(x) {
    lh <- par('cin')[2] * par('cex') * par('lheight')
    inch <- x/2.54
    inch/lh
}

# _____ Function to return a desired sequence
# helper for breaks along axes
my.breaks <- function(my.vector, step){
    my.min <- floor(min(my.vector))
    my.max <- ceiling(max(my.vector))
    seq(from = round(my.min/step)*step, 
        to   = round(my.max/step)*step,
        by   = step)
}

# ==================================
# Plot
# ==================================
# ___ open graphic device with desired parameters
pdf(file = "Plot, type b, inwards ticks, base R.pdf",
    width = 10/2.54, height = 7/2.54, 
    family = "Times", pointsize = 8)
# Since "width" and "height" need to be in inches, one can still use cm 
# and divide by 2.54 to make the conversion to inch.
# family="Times" refers to the font family (here: Times New Roman).
# Check this link for some family fonts: http://www.statmethods.net/advgraphs/parameters.html
# pointsize = 8 refers to the point size used, here (Times New Roman) 8

# ___ storing default par() for reverting later to default values
par.default <- par()

# ___ adjust plotting region
par(mai = c(0.9/2.54, 1.2/2.54, 0.1/2.54, 0.1/2.54))
# mai  - adjust margins of plotting region (Bottom, Left, Top, Right)
# X[cm]/2.54 = inch (or give directly inch values)

# ___ get some min-max values from data
OX.min <- floor(min(DF$year))
OX.max <- ceiling(max(DF$year))
OY.min <- floor(min(DF$mean))
OY.max <- ceiling(max(DF$mean))

# ___ plot empty frame
plot(x = DF$year , y = DF$mean,
     xlab="", xlim = c(OX.min, OX.max),
     ylab="", ylim = c(OY.min, OY.max),
     xaxt="n", yaxt="n", type = "n")

# ___ add two vertical lines
abline(v = c(2010,2013), lty="dashed", lwd=2, col="gray")

# ___ add the points
points(x = DF$year , y = DF$mean,
       xlab="", xlim = c(OX.min, OX.max),
       ylab="", ylim = c(OY.min, OY.max),
       type = "b", lty="solid", cex=1, pch=21, bg="black",
       las = 1, font.lab=2, cex.lab=10/8, xaxt="n", yaxt="n")

# ___ Create custom OX axis
labels.X <- my.breaks(DF$year, step=5)
axis(side=1, at=labels.X, labels=FALSE, tck=0.02)

# position OX labels
text(x=labels.X, y=OY.min-1.5,
     labels = labels.X, pos = 1, xpd = TRUE)
# x & y are graph coordinates (not cm!)
# x- value : adjusting for labels OX positions

# set the title of OX axis at x cm outwards from the plot edge - the one set with par(mai=...) above
title(xlab="Year",line=cm2line(0.55), font.lab=2, cex.lab=10/8)

# ___ Create custom OY axis
labels.Y <- my.breaks(DF$mean, step=10)
axis(side=2, at=labels.Y, labels=FALSE, tck=0.02)

# position OY labels
text(x=OX.min-1.5, y=labels.Y,
     labels = labels.Y, xpd = TRUE)
# x & y are graph coordinates (not cm!)
# x- value : adjusting for labels OX positions

# set the title of OY axis at x cm outwards from the plot edge - the one set with par(mai=...) above
title(ylab="means",line=cm2line(0.75), font.lab=2, cex.lab=10/8)

# return par() to default values (par.default was saved previosly)
par(par.default)

# close the device
dev.off()