RinAction - R Graph Parameter Basics

gistfile1.r

#-----------------------------------------------------------------------------#
#-----------------------------------------------------------------------------#
# R in Action - Working with graphs                                           # 
#-----------------------------------------------------------------------------#
#-----------------------------------------------------------------------------#

setwd <- "C:/RinAction/data/workspace"
setwd <- "C:\RinAction\data\workspace"
mtcars <- read.table("C:/RinAction/data/mtcars.csv", header=TRUE, sep=",")

# pause after each graph
par(ask = TRUE)

install.packages("Hmisc")

########################################
#     Saving Graphs                    #
########################################

pdf("C:/RinAction/data/workspace/mygraph.pdf")
attach(mtcars)
plot(wt,mpg)
abline(lm(mpg~wt))
title("Regression of MPG on Weight")
detach(mtcars)
dev.off()


########################################
#     Simple Examples                  #
########################################

help(plot)
dose <- c(20, 30, 40, 45, 60)
drugA <- c(16, 20, 27, 40, 60)
drugB <- c(15, 18, 25, 31, 40)
plot(dose, drugA, type = "b")

######################################################
#     Saving & Restoring Current Graph Parameters    #
######################################################

oldpar <- par(no.readonly = TRUE)
oldpar

help(par)
par(lty = 2, pch = 17)
plot(dose, drugA, type = "b")
par(oldpar)

######################################################
#                Symbols and lines                   #
#      pch --> symbol type                           # 
#      cex --> symbol size                           #
#      lty --> line   type                           #
#      lwd --> line   width                          #
######################################################

plot(dose, drugA, type = "b", lty = 2, pch = 17)
plot(dose, drugA, type = "b", lyt = 3, lwd = 3, pch = 15, cex = 2)


######################################################
#              --------Colors-----------             #
# col             default plotting color             #
# col.axis        color for axis text                # 
# col.lab         color for axis labels              #
# col.main        color for titles                   #
# col.sub         color for subtitles                #
# fg              foreground color                   #
# bg              background color                   #  
######################################################

# You can specify colors in R by index, name, hexadecimal, RGB, or HSV
# col=1, col="white", col="#FFFFFF", col=rgb(1,1,1), and col=hsv(0,0,1)

# http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf

# Functions that's used to create vectors of contiguous colors: rainbow(), heat.colors(), 
# terrain.colors(), # topo.colors(), cm.colors()

n <- 10
mycolors <- rainbow(n)
pie(rep(1, n), labels = mycolors, col = mycolors)
mygrays <- gray(0:n/n)
pie(rep(1, n), labels = mygrays, col = mygrays)


#################################################################
#                Text characteristics                           #

#      cex --> number indicating the amount by which 
#              plotted text should be scaled relative 
#              to the default                                   # 
#      cex.axis --> magnification of axis text relative to cex  #
#      cex.lab  --> magnification of axis labels relative to cex#
#      cex.main --> magnification of titles relative to cex     #
#      cex.sub  --> magnification of subtitlesls relative to cex#

#      font                                                     #
#      font.axis                                                #
#      font.lab                                                 #
#      font.main                                                #
#      font.sub                                                 #
#      ps   -----> Font point size(roughly 1/72 inch)           #
#           -----> Text size = ps*cex                           #
#      family   ---> font family for drawing text               #
#################################################################

dose <- c(20, 30, 40, 45, 60)
drugA <- c(16, 20, 27, 40, 60)
drugB <- c(15, 18, 25, 31, 40)
opar <- par(no.readonly = TRUE)
par(pin = c(4, 6))
par(lwd = 2, cex = 1.5)
par(cex.axis = 0.3, font.axis = 3)
plot(dose, drugA, type = "b", pch = 19, lty = 2, col = "red")
plot(dose, drugB, type = "b", pch = 23, lty = 6, col = "blue", bg = "green")
par(opar)

# Font family
opar <- par(no.readonly = TRUE)
par(cex = 1.5)
plot(1:7, 1:7, type = "n")
text(3, 3, "Example of default text")
text(4, 4, family = "mono", "Example of mono-spaced text")
text(5, 5, family = "serif", "Example of serif text")
par(opar)

######################################################
#       --------Titles/Axis/Lengends---------        #
# main            title                              #
# subtitle        subtitle                           # 
# xlab            x-axis label                       #
# ylab            y-axis label                       #
# xlim            x-axis range                       #
# ylim            y-axis range                       #
######################################################


#   Title    

plot(dose, drugA, type = "b", col = "red", lty = 2, 
     pch = 2, lwd = 2, main = "Clinical Trials for Drug A", 
     sub = "This is hypothetical data", 
     xlab = "Dosage", ylab = "Drug Response", xlim = c(0, 60), 
     ylim = c(0, 70))

title(main="My title", col.main="red", 
      sub="My Sub-title", col.sub="blue"
      xlab="My X Label", ylab="My Y label"
      col.lab="green", cex.lab=0.75)

# Custom Axes  

x <- c(1:10)
y <- x
z <- 10/x
opar <- par(no.readonly = TRUE)
par(mar = c(5, 4, 4, 8) + 0.1)

plot(x, y, type = "b", pch = 21, col = "red", yaxt = "n", lty = 3)
plot(x, y, type = "b", pch = 21, col = "red", yaxt = "n", lty = 3, ann = FALSE)
lines(x, z, type = "b", pch = 22, col = "blue", lty = 2)
axis(2, at = x, labels = x, col.axis = "red", las = 2)
axis(4, at = z, labels = round(z, digits = 2), col.axis = "blue", las = 2, cex.axis = 0.7, tck = -0.01)
mtext("y=1/x", side = 4, line = 3, cex.lab = 1, las = 2, col = "blue")
title("An Example of Creative Axes", xlab = "X values", ylab = "Y=X")
par(opar)


# Referece Line 
# Lengend       

dose <- c(20, 30, 40, 45, 60)
drugA <- c(16, 20, 27, 40, 60)
drugB <- c(15, 18, 25, 31, 40)
opar <- par(no.readonly = TRUE)
par(lwd = 2, cex = 1.5, font.lab = 2)
plot(dose, drugA, type = "b", pch = 15, lty = 1, col = "red", 
     ylim = c(0, 60), main = "Drug A vs. Drug B", xlab = "Drug Dosage", 
     ylab = "Drug Response")
lines(dose, drugB, type = "b", pch = 17, lty = 2,col = "blue")
abline(h = c(30), lwd = 1.5, lty = 2, col = "grey")
library(Hmisc)
minor.tick(nx = 3, ny = 3, tick.ratio = 0.5)
legend("topleft", inset = 0.5, title = "Drug Type", 
       c("A", "B"), lty = c(1, 2), pch = c(15, 17), col = c("red","blue"))
par(opar)


#   Labeling points      

attach(mtcars)
plot(wt, mpg, main = "Milage vs. Car Weight", xlab = "Weight",
     ylab = "Mileage", pch = 18, col = "blue")
text(wt, mpg, row.names(mtcars), cex = 0.6, pos = 4, 
     col = "red")
detach(mtcars)

# View font families
opar <- par(no.readonly = TRUE)
par(cex = 1.5)
plot(1:7, 1:7, type = "n")
text(3, 3, "Example of default text")
text(4, 4, family = "mono", "Example of mono-spaced text")
text(5, 5, family = "serif", "Example of serif text")
par(opar)


###################################
##      combining graphs         ##
###################################

# Combine Example 1
attach(mtcars)
opar <- par(no.readonly = TRUE)
par(mfrow = c(2, 2))
plot(wt, mpg, main = "Scatterplot of wt vs. mpg")
plot(wt, disp, main = "Scatterplot of wt vs disp")
hist(wt, main = "Histogram of wt")
boxplot(wt, main = "Boxplot of wt")
par(opar)
detach(mtcars)

# Combine Example 2
attach(mtcars)
opar <- par(no.readonly = TRUE)
par(mfrow = c(3, 1))
hist(wt)
hist(mpg)
hist(disp)
par(opar)
detach(mtcars)

# Multi-Chart Layout
attach(mtcars)
layout(matrix(c(1, 1, 2, 3), 2, 2, byrow = TRUE))
hist(wt)
hist(mpg)
hist(disp)
detach(mtcars)

# Multi-Chart Layout control
attach(mtcars)
layout(matrix(c(1, 1, 2, 3), 2, 2, byrow = TRUE), 
       widths = c(3, 1), heights = c(1, 2))
hist(wt)
hist(mpg)
hist(disp)
detach(mtcars)

# Fine placement of figures in a graph

opar <- par(no.readonly = TRUE)
par(fig = c(0, 0.8, 0, 0.8))
plot(mtcars$wt, mtcars$mpg, xlab = "Miles Per Gallon", 
     ylab = "Car Weight")
par(fig = c(0, 0.8, 0.55, 1), new = TRUE)
boxplot(mtcars$wt, horizontal = TRUE, axes = FALSE)
par(fig = c(0.65, 1, 0, 0.8), new = TRUE)
boxplot(mtcars$mpg, axes = FALSE)
mtext("Enhanced Scatterplot", side = 3, outer = TRUE, 
      line = -3)
par(opar)