Module 4 R Charts

D Kelly O'Day R Charts Mod 4 - R Charts: 1

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Module 4R Charts

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Module 4 R Graphics Menu

• Making a Graphic Script

• Working with plot() Function

• Adding Text to a Chart

• Adding Lines to Chart

• Extra R Scripts


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Making a Graphic ScriptMenu

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Making a Graphic Script

• R’s Graphic Packages

• R’s 3 Distinct Chart Areas

• Script Components

– High level functions

– Graphic parameters

– Low level Functions

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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 module shows the traditional - base graphics system

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R’s 3 Distinct Chart Areas

• R’s 3 Chart Areas:

1. Plot Area – within axes

2. Figure Margin Area – for axis labels and tick mark labels

3. Outer Margin Area

• R gives User precise control over content, format of all 3 Areas

– High Level Graphic Functions

– Graphic Parameters

– Low Level Graphic Functions

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Making a Graphic Scriptwith R’s Graphic Package

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” )

# R Script to produce scatter chart

x_data <- ...y_data <-…par( ) # Graphic parameters

plot( ) # High level plot function

text( ) # Low level function

Graphic Parameters 70 GPs defaults set

adjust w/ par()

High Level Graphic Function Call

Use GP defaults or

adj GP w/ argument

Low Level GraphicFunction Call

Use GP defaults or

adj GP w/ argument

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High Level Graphic Functions Produce complete chart

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Type R function()

Bar Chart barplot()

Box & Whisker Plot boxplot()

Dot Plot dotchartt()

Histogram hist()

Scatter Plot plot()

Strip Chart stripchart()

This module focuses on plot() function low level functions, graphic parameters.

Module 5 covers box, dot, histogram and strip charts


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Low Level Plot FunctionsAdd graphic content to current plot

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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

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)

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


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Graphic ParametersGP

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

– name: col = – value: “red”

• Default Values Set At start of R session

• To Get par() values– par() lists all 70 with current

value– par(“GP_name”) gives current

value for specific GP• User can change GP value:

– Global: par(“col” = “red”)– Local: plot(x,y, col=“red”)

> par(“col”)[1] “black”

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

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adj= 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” = full

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 row

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


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pch = Plot Characters Graphic Parameter

• R has 25 plotting characters

• pch = specifies plot character

• Characters 19 – 20 can be filled with selected color

o 19 – Solid circle

o 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 Menu

• 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”

•


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Assignment 4-1Getting Familiar with par()

1. Print out par documentation ?par2. Get Current Values for all par()3. Get current par(“bty”) value

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Working with plot() Function


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plot() Function ArgumentsMenu

x,y

y~xVectors for x and y values to be plotted

type=

type = “p” – individual points

type = “l” – line

type = “b” – points connected with lines

type = “h” – vertical lines from 0

type = “s” – step chart

main = “ ”

sub = “ ”

Figure title top of plot, large font

Sub title – below X axis, smaller font

xlab = “ ”

ylab = “ ” X and Y axis titles

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

plot(x,y, type=“?”, main’”??”, sub = “??“, xlab=“??”, ylab =“??”, ann =?, axes = ?, xlim = c(x1,x2), ylim = c(y1,y2))

or

plot(y ~ x, data = “??”, type=“?”, main’”??”, sub = “??“, xlab=“??”, ylab =“??”, ann =?, axes = ?, xlim = c(x1,x2), ylim = c(y1,y2))


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plot() Function DefaultsMenu

Potential plot() Default Improvements1. Line – symbol style2. X & Y axis do not meet @ 03. Remove box around plot4. Adjust Y axis label orientation5. Improve X & Y axis labels

# R script to demonstrate default plot()

## Ex_Scr_4_1_default_plot.R ################### ##Script to produce default XY plot()## STEP 1: SETUP - Source File 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 DATA y_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)


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Improving plot() Function Defaultswith Additional plot() arguments & graphical parameters

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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

– “red”

– “blue”

– “darkgreen”

• To get list of R colors:

>colors()

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

• Alternatives: rgb() and hsv()

• Color Conversions:

– col2rgb()

– convertColor()

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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

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Example Scatter plot

## Ex_Scr_4_3_xy_plot.R ################### ##Script to produce scatter plot## STEP 1: SETUP - Source File rm(list=ls()); par(oma=c(2,1,0,1)) script <- "C:/Learn_R/Mod_4_R_Charts/Ex_Scr_4_3_xy_plot.R"## STEP 2: READ DATA x_data <- seq(0,10*pi,0.1*pi) y_data <- sin(x_data)plot(x_data,y_data,type = "l")## 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(date(), side = 1, line =.75, cex = 0.7, outer = T, adj = 1)

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Assignment 4-2xy plot ()

• Start R Session

• In R Console, Open Script:“C:/Learn_R/Mod_4_R_Script/Ex_Scr_4_3_xy_plot.R”

• Save as:“C:/Learn_R/Mod_4_R_Script/Practice_4_1_xy_plot.R”

• Make these changes– par() settings:

• par(ps = 10)• par(las = 1)

– plot() formatting:– type = “b”– pch = 16– col = “blue”– xlab = “X”; ylab= “sin(X)”– main = “xy Plot of sin() Formula”– xlim = c(0, 15)– ylim = c(-2, 2)

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Expected Result


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Assignment 4-2xy plot ()

## Practice_4_1_xy_plot.R ################### ##Script to produce scatter plot## STEP 1: SETUP - Source File rm(list=ls()); par(oma=c(1.75,1,0,1)); par(las=1); par(ps=10) script <- "C:/Learn_R/Mod_4_R_Charts/Practice_4_1_xy_plot.R"## STEP 2: READ DATA x_data <- seq(0,10*pi,0.1*pi) y_data <- sin(x_data)plot(x_data,y_data,type = "b",pch = 16,

col = "blue", xlab ="X", ylab = "sin(X)",main = "xy Plot of sin() Function",xlim = c(0,15), ylim = c(-2,2))

## Outer margin annotation my_date <- format(Sys.time(), "%m/%d/%y") mtext(script, side = 1, line = .5, cex=0.7, outer = T, adj = 0) mtext(date(), side = 1, line =.5, cex = 0.7, outer = T, adj = 1)

Assignment 4-2Script

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Assignment 4-3Make Step Chart and Scatter Plot

Interactively Edit Your Practice_4_1_xy_plot.R Script to make these charts

type = ‘s” type = ‘p”

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Working With TextMenu

Text is Critical for chart interpretation



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Working With Text

• Text Additions:

– main= argument to add chart 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 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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Text is Critical for chart interpretation


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Adding text string in Plot Areatext () Function

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

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

“note” – text to be added to plot pos – position of text with respect to

x, y coordinates. Default is centered on point.

cex - font magnification factor col - color srt – text rotation - degrees

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• User can construct multi-line text strings by using \n to designate new line

• Note <- “This is an example \n of a multi-line note ”

\n for Multi-line Text

\”to add quote marks to text string

• Text strings designated by “ “ marks• 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”


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Simple Plot – No Annotation

#################### Example R Script: ################# Ex_Scr_4_4_simple_plot.R ##########################Script to read data file, simple plot ## STEP 1: SETUP - Source File rm(list=ls()); oldpar<- par(no.readonly=T); ;par(las=1)link <- "C:\\Learn_R\\Mod_4_R_Charts\\Data_4_1_GISS_1980_By_year.txt.txt"

## STEP 2: READ DATA my_data <- read.table(link, skip =0, sep = ",", dec=".", row.names = NULL , header = F, colClasses = c("numeric","numeric"), comment.char = "#", na.strings = c( "","*", "-",-99.9, -999.9 ), col.names = c( "yr", "anom") ) attach(my_data)## STEP 3: MANIPULATE DATA## STEP 4: PRODUCE PLOT - REPORT plot(yr, anom, type = "l", col = "red")## Outer margin annotation my_date <- format(Sys.time(), "%m/%d/%y") mtext(script, side = 1, line = .5, cex=0.7, outer = T, adj = 0) mtext(my_date, side = 1, line =.5, cex = 0.7, outer = T, adj = 1)## STEP 5: CLOSE par(oldpar) detach(my_data)

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Simple Plot –with Annotation

#################### Example R Script: ################# Ex_Scr_4_5_simple_plot_w_annotation.R ######################## ##Script to read data file, simple plot ## STEP 1: SETUP - Source File rm(list=ls()) script<- "C:\\Learn_R\\Mod_4_R_Charts\\Ex_Scr_4_5_simple_plot_w_annotation.R" oldpar<- par(no.readonly=T) par(oma=c(2,2,1,2)); par(las=1); par(mar=c(5,4,2,1)) link <- "C:\\Learn_R\\Mod_4_R_Charts\\Data_4_1_GISS_1980_By_year.txt.txt"## STEP 2: READ DATA my_data <- read.table(link, skip =0, sep = ",", dec=".", row.names = NULL , header = F, colClasses = c("numeric","numeric"), comment.char = "#", na.strings = c( "","*", "-",-99.9, -999.9 ), col.names = c( "yr", "anom") ) attach(my_data)## STEP 3: MANIPULATE DATA m_title <- "GISS Temperature Anomaly - C (1980-2008)" sub_title <- "Source: http://data.giss.nasa.gov/gistemp/" note <- "Baseline 1951-1980"## STEP 4: PRODUCE PLOT - REPORT plot(yr, anom, type = "l", col = "red", main = m_title, sub = sub_title, ylab = " Temperature Anomaly - C", xlab = "", cex.axis = 0.75, cex.lab=0.8, cex.main = .8, cex.sub = 0.6) text(1985,0.65, note, cex=0.6 ) my_date <- format(Sys.time(),"%m/%d/%y") mtext(script, side=1, line = .5, outer = T, adj = 0, cex = 0.65) mtext(my_date, side = 1, line = 0.5, outer = T, adj = 1, cex = 0.7)## STEP 5: CLOSE par(oldpar); detach(my_data)

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text()font & 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

= “sans”

= “serif”

= “mono”

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paste() Functionconcatenates arguments into a single string

paste(arg1, arg2, arg3, sep= “ ”)

arg1 – text string or variable to be concatenated with other arguments

sep = “ ” - separator to add between arguments. Space good for text.

Variable data and text strings can be

concatenated into a single string that can

then be added to plot with text()

Example:

# build text string with paste()

my_date <- paste(“today is “, date())

# add text string to plot

text(x, y, my_date, col = “red”)

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Adding Text within Margin Area

mtext( “note”, side = , line = , 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

• outer – use outer area (T or F)

• adj – text alignment, 0 = left, 0.5= center, 1 = right

• cex - font adjustment factor

• col - color

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1

2

3

4AxisSides

Axis Numbering Convention


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How I’ve Been Adding Margin Text to Each Mod 4 Plot

3 Steps to Create Margin Annotation:

• Set Outer Margin Areas

par(oma=c(2,2,0,1))

• Establish script name vector

script<- "C:\\Learn_R\\Mod_4_R_Charts\\Ex__plot_.R"

• Develop Margin Text w/date & script name

## Outer margin annotation my_date <- format(Sys.time(), "%m/%d/%y") mtext(script, side = 1, line = .5, cex=0.7, outer = T, adj = 0) mtext(my_date, side = 1, line =.5, cex = 0.7, outer = T, adj = 1)

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Assignment 4-4Annotate Simple Chart Yourself

• Start R Session

• In R Console, Open Script:“C:/Learn_R/Mod_4_R_Script/

Ex_Scr_4_3_simple_plot.R”

• Save as:“C:/Learn_R/Mod_4_R_Script/Practice_4_2_my_simple.R”

• You’ve seen me do it

• Make the Full Annotation on your own

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Adding Lines in Plot AreaMenu



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Adding Lines in Plot AreaMenu

#################### Example R Script: ################# Ex_Scr_4_6_add_lines_to_plot.R ##########################Script to read data file, simple plot no annotation ## STEP 1: SETUP - Source File rm(list=ls()) script<- "C:/Learn_R/Mod_4_R_Charts/Ex_Scr_4_6_add_lines_to_plot.R"

oldpar<- par(no.readonly=T) ; par(las=1) par(ps=10); par(oma=c(2,2,1,2)) ## STEP 2: READ DATAx <- 0:100; y <- x^2x_pts <- c(15, 35, 35, 15, 15); y_pts <- c(8300, 8300, 6500, 6500,8300)# STEP 3: MANIPULATE DATA# STEP 4: PRODUCE CHART - REPORTplot(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)lines(x_pts, y_pts, lty=1, col = "green")points(x_pts,y_pts, type = "p",col ="red",pch=19)

my_date <- format(Sys.time(),"%m/%d/%y") mtext(script, side=1, line = .5, outer = T, adj = 0, cex = 0.65) mtext(my_date, side = 1, line = 0.5, outer = T, adj = 1, cex = 0.7)## STEP 5: CLOSE par(oldpar) detach(my_data)


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Assignment 4-5Working with grid(), points(), abline(), arrows() & lines()

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• Start R Session

• In R Console, Open Script:“C:/Learn_R/Mod_4_R_Script/Ex_Scr_4_6_add_lines_to_plot.R”

• Save as:“C:/Learn_R/Mod_4_R_Script/Practice_4_3_add_lines_to_plot.R”

• You’ve seen me work with it

• Changes each element to see what happens, get comfortable with forms of lines

Printout & Read R Documentation for lines

? grid()? points()? lines()? abline()? arrows()


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Extra Scripts


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Plot Box and Axis Styles

• Plot Box & Axis Options– Box type

• bty=“n”• bty=“o”

– Axes• axes = T or F

– Axis Offset: • xaxs= “i” or “r”• yaxs = “i” or “r”

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

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Module 4 R Charts