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Week 14 Lecture:Week 14 Lecture:Graphics in R

Introduction to Programming and Geoprocessing Using R

GEO6938‐4172GEO4938‐4166

Overview

• R can plot data and draw graphics…b t l t f th ft… but so can lots of other software.

• So why choose R?

Customizable, extensible, programmable graphicsgraphics

R is permissive…

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R’s Graphics Ecosystem

• R’s Graphic Packages• R s Graphic Packages

• R’s 3 Distinct Chart Areas

• Script Components• Script Components – High level functions– Graphic parameters– Low level functions

Low Level Graphics

• R follows a “painters” model• We can add items like we would add ink/paint• R’s base graphics provide primitive graphics elements:

• Graphs and charts are just these elements arranged in meaningful ways

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R’s  Graphics Packages

• R has several graphics subsystems:– graphics, traditional graphics– grid package (low level functions)– lattice package– ggplot2 package

• This lecture will cover the traditional, graphics system and a bit about ggplot2

R’s Graphics Ecosystem

• R’s core graphics capabilities focus on static, 2D l t2D plots

grDevices

grid

lattice ggplot2

graphics

• Possible to produce 3D and animated plots with other packages (e.g. misc3d, rgl)

lattice ggplot2

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R’s Three Distinct Chart Areas

• R’s 3 Chart Areas:1. Plot Area – within 

axesaxes2. Figure Margin Area

– for axis labels and tick mark labels

3. Outer Margin Area

• R gives User precise control over content, f f llformat of all 3 Areas– High Level Graphic 

Functions– Graphic Parameters– Low Level Graphic 

Functions

Based on D Kelly O’Day’s Learn R Workshop, R Charts

Making a Graphic Scriptwith R’s Base Graphic Package 

# R Script to produce scatter chartx_data <- ...data <

High Level GraphicFunction CallUse GP defaults

Low Level  Graphicll y_data <- ...

## Graphic parameterspar( )## High level plot functionplot( ) ## Low level functiontext( )

Graphic Parameters 70 GPs defaults set adjust 

w/ par() 

Use GP defaultsor

w/ argument 

Function  CallUse GP defaults 

orw/ argument

par(oma=c(2,2,2,2)); par(mar=c(3,3,1,1))

plot(x_data, y_data, main = "My Chart Title", type = "b", xlim = c(0,11), ylim = c(0,11), xlab ="X", ylab = "Y", pch=16, col = "red", bty = "n", xaxs="i", yaxs = "i", las=1)

text(2,7, "my note", col = "blue" )

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par(oma=c(2,2,2,2))par(mar=c(3,3,1,1))

Making a Graphic Scriptwith R’s Base Graphic Package 

plot(x_data, y_data, main = "My Chart Title", type = "b", xlim = (0,11), ylim = c(0,11), xlab ="X", ylab = "Y", pch=16, col = "red", bty = "n", xaxs="i", yaxs = "i",las=1)

text(2,7, "my note", col = "blue" )

High Level Graphic Functions

Type R function()Type ()

Bar Chart barplot()

Box & Whisker Plot boxplot()

Dot Plot dotchartt()

Histogram hist()

High level functions produce complete charts…

We’re focusing on plot() and its "low" level functions, graphic parameters…

Scatter Plot plot()

Strip Chart stripchart()

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Low Level Plot FunctionsAdd graphic content to current plot

grid(nx, ny) Add grid lines to current plot.  NA stop grid in corresponding direction

axis(side n,) Add axis at side n to current plot ( ,) p

box(which=, ) Add box around current plot, figure or outer margin area depending on which specified

legend Add legend to current plot

arrows(x,y)lines(x, y)points(x,y)

Add arrow line, line or points to current plot.    type = can be used to specify style ("p","b", "l", etc)

abline(a b) Add li t t l t i i t t b i labline(a,b)abline(h= or v=)

Add line to current plot. a is intercept, b is slope.h/v for horizontal/ vertical  line 

segments(x0,x1,y0, y1) Add line segment(s) between pairs of points

polygon(x,y) Add polygon defined by vectors x and y

text(x,y, "note") Add text to current plot at x & y

Graphic Parameters (GP)• R has over 70 Graphic Parameters (GP)• Each GP has:

name: col =– name: col =– value: "red"

• Default values set at start of an R session

• To get  par() values:– par() lists all GPs with current value– par("GP_name") gives current 

value for specific GP> par("col")[1] "black"

• User can change GP values:– Global: 

par("col" = "red")

– Local: plot(x,y, col="red")

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Essential  Graphical Parametersadj= Text string justification: 0=left, 0.5=centered, 1=right

ann= T or F controls plot annotation

bg= Background color

bty= Type of box around plot: "n"=none,  "l" = x & y, "o" = fully yp p , y,

cex= Magnification ratio for text relative to default point size

col= Color specification. R accepts "red", "blue", "dark grey", etc names for 657 colors

las= Style of tick mark labels: 0=parallel to axis, 1 =always horizontal, 3=always vertical

lty= Line type: 0=blank, 1=solid, 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash

lwd= Line width, default is 1. 

* mar=, oma= Vector c(b,l,t,r) that sets number of lines for margin and outer margin areas by axis #

* mfcol=, mfrow= Vector c(nr,nc) to specify multiple plots. mfcol draws by columns, mfrow by rowmfrow=

pch= Integer specifying a symbol to be used in plotting points

* ps= Point size of text, not symbols

* pty= Plot region: s=square, m=maximum

srt= String rotation in degrees

* xaxs=, yaxs= Style of axis: "r" = offset of x & y to prevent points overplotting axis, "i" = no offset 

* These parameters must be set with call to par().

pch =  Plot Characters Graphic Parameter

• R has 25  plotting characters• pch =  specifies plot character • Characters 19 – 20 can be filled 

with selected coloro 19 – Solid circleo 20 – Bullet circle

• Characters 21: 25 can have selected fill and border colors

bg =  Controls Border color col= Controls fill

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lty= Line Type Graphic Parameter

• R has 6  line types • lty = specifies the line type

• lty= can be specified as integer or character string:0 – "blank"1 – "solid"2 – "dashed"3 – "dotted"4 – "dotdash"5 – "longdash"6 – "twodash" 

plot() Function  Argumentsx,yy~x

Vectors for x and y values to be plotted

type = "p" individual points

plot(x,y, type="?",main = "??", sub = "??",

type=

type =  p  – individual pointstype = "l" – linetype = "b" – points connected with linestype = "h" – vertical lines from 0 type = "s" – step chart

main = " " sub = " "

Figure title top of plot, large fontSub title – below X axis, smaller font

xlab = " "ylab = " "

X and Y axis titles

sub ?? , xlab ="??", ylab ="??", ann = ?,axes = ?,xlim = c(x1,x2), ylim = c(y1,y2))

or

plot(y ~ x, data = "??", ylab = " "

ann= T or F Should default annotation be included

axes = T or F Set to F when you want custom axis

xlim=c( x1, x2)ylim=c(y1, y2)

Limits of plot for X and Y axes

p ot(y , data ,type="?", main="??", sub = "??",xlab="??", ylab ="??", ann = ?,axes = ?,xlim = c(x1,x2), ylim = c(y1,y2))

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plot() Function Defaults## Ex_Scr_4_1_default_plot.R ################### ##Script to produce default XY plot()## STEP 1: SETUP - Source File rm(list=ls())rm(list=ls())par(oma=c(2,1,0,1))script = "C:/Learn_R/Mod_4_R_Charts/Ex_Scr_4_1_default_plot.R"

## STEP 2: READ DATAy_data <- c(0,1,2,3,4,5,6,7,8,9,10,9,8,7,6,5,4,3,2,1,0)x_data <- seq(0:20)

## STEP 3: MANIPULATE DATA

## STEP 4: PRODUCE CHART - REPORT plot(x_data,y_data, main = "plot() Defaults ")

## Outer Margin annotation my_date <- format(Sys.time(), "%m/%d/%y")mtext(script, side = 1, line = .75, cex=0.7, outer = T, adj = 0)mtext(my_date, side = 1, line =.75, cex = 0.7, outer = T, adj = 1)

plot() Function Defaults

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Adding Text within  Margin Area

mtext( "note", side = , line = dj 0 1, outer = F, adj = 0, cex = 1,

col = "red")

• "note" – text to be added to margin area

• side – side of plot to place text(1= bottom, 2= left, 3= top, 4=right)

• line – line of margin to place text, starting at 0, counting outwards

AxisSides

1

2

3

4

Axis Numbering Convention

• outer – use outer area (T or F)• adj – text alignment, 0 = left, 0.5=  

center, 1 = right• cex ‐ font adjustment factor• col  ‐ color 

Improving plot() Function Defaults

plot(x_data,y_data, main = "plot() Defaults" )

plot(x_data,y_data,main = "plot() Default Improvements", type = "b", col = "red", bty = "n", xaxs="i", yaxs = "i", las=1,xlim = c(0,25), ylim = c(0,12), xlab = "X", ylab = "Y" )

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Working With R Colors

• Users can specify colors by name; R has 657 colors

• col = most common way to specify color for lines, points, text

– "red"– "blue"– "darkgreen"

• To get list of R colors:>colors()  

• Alternatives:  rgb() and hsv() 

• Color Conversions:– col2rgb()– convertColor()

plot()  type argument type=?• "p" for points• "b" for both • "o" for both ‘overplotted’ • "l" for lines • "c" for the lines part alone of "b"• "h" for high‐density vertical lines • "s" for h/v stair steps • "S" for v/h stair steps • "n" for no plotting o o p ott g

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Example Scatter plot

################### ##Script to produce scatter plot## STEP 1 SETUP S Fil## STEP 1: SETUP - Source File par(oma=c(2,1,0,1))

## STEP 2: READ DATAx_data <- seq(0,10*pi,0.1*pi)y_data <- sin(x_data)

plot(x_data,y_data,type = "l")

Working With Text

Text Additions:– main= argument to add chart  • Size: par(ps=10)

title in figure margin at top– sub= argument to add subtitle 

below X axis – text() – low level function to add 

text in plot area– mtext() – low level function to 

add text in margin and outer areas

Size:  par(ps 10)• Magnification: cex = 0.85• Color: col="red" (657 named color choices)

• font= 1‐4 (regular, bold, italic, bold italic)• family= ("sans", "serif", "mono")• Alignment: adj = 0,.5,1(left,center, right)• Rotation: srt=

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Adding text string in  Plot Areatext () Function

text( x, y, "note", pos =0, cex = 1, col = "red" srt = 45)

• User  can construct multi‐line text \

\n for Multi-line Text

col = "red", srt = 45)

x,y – plot area coordinates where text should be placed

"note" – text to be added to plotpos – position of text with respect to x, y 

coordinates. Default is centered on point. 

strings by using \n to designate new line

Note <- "This is an example \nof a multi-line note "

\" to add quote marks to text string

• Text strings designated by " " marksUser can embed q ote marks ithin te t

cex ‐ font magnification factorcol  ‐ color srt – text rotation ‐ degrees

• User can embed quote marks within text string by using \" to have R not treat mark as begin/end of text string

Note <- "This is an example of using\"quote marks\" within text string"

text() font and family• font= font type for plot text

=1  Standard =2  Bold=3  Italic=4  Bold and italic

• Use for other figure text– font.axis; font.lab– font.main; font.sub

• family controls font family• family = controls font family= "sans"= "serif"= "mono"

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Adding Lines in Plot Areax <- 0:100y <- x^2x_pts <- c(15, 35, 35, 15, 15)y_pts <- c(8300, 8300, 6500, 6500,8300)

plot(x,y, type = "n", main="Add Lines, Points, Arrows Examples")

points(x, y,col = "black", lty=1, type = "l")

grid(col="lightgrey", lty=1)

abline(h=2500, col="red")abline(v=50, col = "blue")

arrows(65,8400, 85,8400, code=3, col="orange", length = 0.1)g , g )

lines(x_pts, y_pts, lty=1, col = "green")

points(x_pts,y_pts, type = "p",col ="red",pch=19)

Plot Box and Axis Styles 

• Plot Box & Axis Options– Box type ox type

• bty="n"• bty="o"

– Axes• axes = T or F

– Axis Offset: • xaxs= "i" or "r"

"i" " "• yaxs = "i" or "r"

– Axis 3 & 4 tick marks• Axis(n,  tick=T)

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Adding Mathematical Expressions

Basic graphics functions in Rabline Add Straight Lines to a Plotarrows Add Arrows to a Plotassocplot Association PlotsaxTicks Compute Axis Tickmark Locationsaxis Add an Axis to a Plotaxis.POSIXct Date and Date-time Plotting Functionsbarplot Bar Plotsbox Draw a Box around a Plotboxplot Box Plotsbxp Draw Box Plots from Summariescdplot Conditional Density Plotscontour Display Contourscoplot Conditioning Plotscurve Draw Function Plotsdotchart Cleveland Dot Plotsfilled.contour Level (Contour) Plotsfourfoldplot Fourfold Plotsframe Create / Start a New Plot Framegrid Add Grid to a Plothist Histogramshist.POSIXt Histogram of a Date or Date-Time Object

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Basic graphics functions in R

identify Identify Points in a Scatter Plotimage Display a Color Imagelayout Specifying Complex Plot Arrangementslegend Add Legends to Plotslines Add Connected Line Segments to a Plotlocator Graphical Inputmatplot Plot Columns of Matricesmosaicplot Mosaic Plotsmtext Write Text into the Margins of a Plotpairs Scatterplot Matricespanel.smooth Simple Panel Plotpar Set or Query Graphical Parameterspersp Perspective Plotsp p ppie Pie Charts

Basic graphics functions in Rpoints Add Points to a Plotpolygon Polygon Drawingrect Draw One or More Rectanglesrug Add a Rug to a Plotscreen Creating and Controlling Multiple Screens on a

Single Devicesegments Add Line Segments to a Plotspineplot Spine Plots and Spinogramsstars Star (Spider/Radar) Plots and Segment Diagramsstem Stem-and-Leaf Plotsstripchart 1-D Scatter Plotsstrwidth Plotting Dimensions of Character Strings and

Math Expressionssunflowerplot Produce a Sunflower Scatter Plotpsymbols Draw Symbols (Circles, Squares, Stars,

Thermometers, Boxplots) on a Plottext Add Text to a Plottitle Plot Annotationxinch Graphical Units

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Basic graphics functions in R

Generic function plot and its class‐specific methods:

plot Generic X-Y Plottingplot.data.frame Plot Method for Data Framesplot.default The Default Scatterplot Functionplot.design Plot Univariate Effects of a

'Design' or Modelplot.factor Plotting Factor Variablesplot.formula Formula Notation for Scatterplotsplot.histogram Plot Histogramsplot.histogram Plot Histogramsplot.table Plot Methods for 'table' Objectsplot.window Set up World Coordinates for

Graphics Windowplot.xy Basic Internal Plot Function

ggplot2

• High level plotting functionality• Provides a graphical “language” for building very nice figures

• Has a good book out now explaining the philosophy behind it:

http //had co nz/ggplot2/http://had.co.nz/ggplot2/

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ggplot2 Exampledata(mpg)ggplot(mpg, aes(displ, hwy))+

geom_point()+geom_line(aes(color = factor(cyl)))

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ggplot2 Examples

p <- ggplot(mpg, aes(displ, hwy))p + geom point() + stat smooth()p + geom_point() + stat_smooth()

ggplot2 Examples

By default, stat_smooth() has added a loess line ith th t d d t d b iwith the standard error represented by a semi‐

transparent ribbon. You could also specify the method to use to add a different smoothing line:

p + geom_point() + stat_smooth(method = "lm")

library(MASS)p + geom_point() + stat_smooth(method = "rlm")

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ggplot2 Shortcut

• qplot() is the “simple” version of ggplot() d i tand is very easy to use:

qplot(x=ShotDist, geom="histogram", fill=as.factor(DistToPin), main="Distribution of Accurate Shot Distances (< 20 yds.) by Shot Distance", binwidth=10, data=subset(raw_data, BallToPinDist < 20))

Distribution of Accurate Shot Distances (< 20 yds.) by Shot Distance

8

coun

t

4

6

as.factor(DistToPin)

125

150

175

ShotDist

0

2

100 120 140 160 180

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For further information:• "R Graphics, Second Edition"

http://www.stat.auckland.ac.nz/~paul/RG2e/

• “Learn R Toolkit”http://chartsgraphs wordpress com/learnr toolkit/http://chartsgraphs.wordpress.com/learnr‐toolkit/

• "Lattice: Multivariate Data Visualization with R"http://lmdvr.r‐forge.r‐project.org/

• "ggplot2: Elegant Graphics for Data Analysis"http://had.co.nz/ggplot2/book/

• The Graphics CRAN Task Viewhttp://cran.r‐project.org/web/views/Graphics.html

• The R Graphics Galleryp yhttp://addictedtor.free.fr/graphiques/

• Advance Charts for Climate and Process Trendshttp://processtrends.com/toc_r.htm

• The R Graphical Manualhttp://www.oga‐lab.net/RGM2/