# Statistical Methods in Medical Research
# Laaketieteellisen tutkimuksen tilastolliset menetelmat
# At University of Helsinki
# 22.8.2023
# Matti Pirinen


###
### 7. Learn R: Plotting part II
###

# Let's go through some more of the basic plotting options.

# Let's generate data with n = 10 points from two Normal distributions
set.seed(11) #initialize the random number generator
n = 10
x = rnorm(n, rep(c(-1,3), each = n/2), 1) #mean = -1 for first 5 and = +3 for last 5; sd = 1 for all
y = rnorm(n, rep(c(-1,1), each = n/2), 1) #mean = -1 for first 5 and = +1 for last 5; sd = 1 for all

plot(x,y)

# We can give different color and style for every point in the plot 
# by making 'col =' and 'pch =' vectors of length 'n'
# Let's use blue dots for 1,...,5 and red triangles for 6,...,10.
plot(x, y, col = rep(c("steelblue","firebrick"), each = n/2), 
     pch = rep(c(19, 17), each = n/2))

# Command:
colors() 
# lists some readily available color names and you can see them for example here:
# https://www.datanovia.com/en/blog/awesome-list-of-657-r-color-names/

# The possible pch styles are here:
# https://www.datanovia.com/en/blog/pch-in-r-best-tips/
  

# Once a plot exists, we can add things to it, 
# rather than always draw a new plot

# ADDING STRAIGHT LINES
# Let's add line y = 2*x - 2
abline(a = -2, b = 2, col = "black", lty = 2) # 'lty' defines line type, lty = 2 is a dashed line
# Let add horizontal line at y = 0
abline(h = 0, col = "gray", lty = 3)
# Let's add vertical line at x = 1
abline(v = 1, col = "gray", lty = 3)

# ADDING GRID ON BACKGROUND
grid() 
# NOTE: You might want to add grid before plotting points so that the grid is
#       behind the points and not on top of the points like here.

# ADDING TEXT to given x-y coordinate positions
text(x = c(2,-1.2), y = c(1.2,-2), c("A", "B"), col = c("limegreen","tomato"))
# This way you can label individual points, for example.

# ADDING LINE SEGMENTS
# We can add segments connecting a set of x and y coordinates by lines(x,y)
lines(x = c(-2,-2,2,2), y = c(0,-1,-1,-2), lty = 1)
# This is also a good option for adding graphs of functions as long as we have 
# small enough intervals between x-coordinates so that graph appears continuous (See Lecture 4).

# ADDING POINTS
# Let's add points at (0,0), (0,1) 
points(x = c(0,1), y = c(0,0), pch = 18, col = "orange", cex = 1.4)

# ADDING LEGEND
# We can add legend to four corners, such as "bottomright" or "topleft" (or to any x-y position)
# Let's add line legend to topleft
# pch for lines can be -1, although would not be needed here since only lines are included in this legend
legend("topleft", legend = c("line", "dashed"), cex = 0.85,
       pch = c(-1, -1), lty = c(1, 2), col = c("black", "black"))
# And point legend to bottomright
# lty for non-line symbols are 0, although wouldn't be needed in this legend since only points are present
legend("bottomright", legend = c("dots","tris", "extra"), cex = 0.85,
       pch = c(19, 17, 18), lty = c(0, 0, 0), col = c("steelblue", "firebrick", "orange"))
# You may need to adjust cex to get it as suitably sized for your purpose.



#####
##### R Graph Gallery
#####

# R is well-known for endless possibilities to make really good plots about the data.
# Have a look at
# https://r-graph-gallery.com/
# for some examples of some common plotting tasks done with R.

# NOTE: Many of the plots in the gallery are using 'ggplot2' package which has its own
# logic and command syntax that we haven't been learning on this course.
# We can do all the basic things also with the base R
# plotting that we have been using on this course.
# It is just good to have an idea what else can be done if you will ever need to.