Lecture 5 - ANT 191
Damien Caillaud
4/15/2019
Basic scatter plots in R
Download the iris.csv file from canvas and load it in R. To do so, modify the line of code below (hint: remember the “import dataset” menu?):
dat <- read.csv(file="~/Downloads/Iris (2).csv", header=T)Now create a scatterplot with 3 colors:
head(x=dat, n=10)## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
## 7 4.6 3.4 1.4 0.3 setosa
## 8 5.0 3.4 1.5 0.2 setosa
## 9 4.4 2.9 1.4 0.2 setosa
## 10 4.9 3.1 1.5 0.1 setosaplot(y=dat$Sepal.Length, x=dat$Petal.Length)
myColorVector <- ifelse(dat$Species == "setosa", "red", ifelse(dat$Species=="versicolor", "blue", "green"))
plot(dat$Sepal.Length, dat$Petal.Length, col= myColorVector)
plot(dat$Sepal.Length, dat$Petal.Length, col= c(rep("red", 50), rep("blue", 50), rep("green", 50)))#monique's solution
#third solution
plot(x=dat$Sepal.Length, y=dat$Petal.Length, type="n")
points(dat$Sepal.Length[dat$Species=="setosa"], dat$Petal.Length[dat$Species=="setosa"], col="red")
points(dat$Sepal.Length[dat$Species=="virginica"], dat$Petal.Length[dat$Species=="virginica"], col="blue")
points(dat$Sepal.Length[dat$Species=="versicolor"], dat$Petal.Length[dat$Species=="versicolor"], col="green")
Let’s play with the “type” argument:
## Playing with the "type" argument
plot(dat$Petal.Length, dat$Sepal.Length, type="n", xlab="petal length", bty="l") ## Here we're creating an initial blank plot. Look at the help section for the function plot for details about the argument "type"
points(dat$Petal.Length[dat$Species=="setosa"], dat$Sepal.Length[dat$Species=="setosa"], type="o")
points(dat$Petal.Length[dat$Species=="virginica"], dat$Sepal.Length[dat$Species=="virginica"], type="h")
subsetting tables and vectors using the square brackets [ ]
Why did we just use square brackets? This is how you subset data from a vector or dataframe. In other words, you want to extract only certain elements from your dataset. Note that you would use [ , ] if you are specifying a row and column in a dataframe. For example the value in the 4th row and 1st column can be subsetted using:
dat[dat$Species=="setosa",2]## [1] 3.5 3.0 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 3.7 3.4 3.0 3.0 4.0 4.4 3.9
## [18] 3.5 3.8 3.8 3.4 3.7 3.6 3.3 3.4 3.0 3.4 3.5 3.4 3.2 3.1 3.4 4.1 4.2
## [35] 3.1 3.2 3.5 3.6 3.0 3.4 3.5 2.3 3.2 3.5 3.8 3.0 3.8 3.2 3.7 3.3dat[dat$Species=="setosa",]## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
## 7 4.6 3.4 1.4 0.3 setosa
## 8 5.0 3.4 1.5 0.2 setosa
## 9 4.4 2.9 1.4 0.2 setosa
## 10 4.9 3.1 1.5 0.1 setosa
## 11 5.4 3.7 1.5 0.2 setosa
## 12 4.8 3.4 1.6 0.2 setosa
## 13 4.8 3.0 1.4 0.1 setosa
## 14 4.3 3.0 1.1 0.1 setosa
## 15 5.8 4.0 1.2 0.2 setosa
## 16 5.7 4.4 1.5 0.4 setosa
## 17 5.4 3.9 1.3 0.4 setosa
## 18 5.1 3.5 1.4 0.3 setosa
## 19 5.7 3.8 1.7 0.3 setosa
## 20 5.1 3.8 1.5 0.3 setosa
## 21 5.4 3.4 1.7 0.2 setosa
## 22 5.1 3.7 1.5 0.4 setosa
## 23 4.6 3.6 1.0 0.2 setosa
## 24 5.1 3.3 1.7 0.5 setosa
## 25 4.8 3.4 1.9 0.2 setosa
## 26 5.0 3.0 1.6 0.2 setosa
## 27 5.0 3.4 1.6 0.4 setosa
## 28 5.2 3.5 1.5 0.2 setosa
## 29 5.2 3.4 1.4 0.2 setosa
## 30 4.7 3.2 1.6 0.2 setosa
## 31 4.8 3.1 1.6 0.2 setosa
## 32 5.4 3.4 1.5 0.4 setosa
## 33 5.2 4.1 1.5 0.1 setosa
## 34 5.5 4.2 1.4 0.2 setosa
## 35 4.9 3.1 1.5 0.2 setosa
## 36 5.0 3.2 1.2 0.2 setosa
## 37 5.5 3.5 1.3 0.2 setosa
## 38 4.9 3.6 1.4 0.1 setosa
## 39 4.4 3.0 1.3 0.2 setosa
## 40 5.1 3.4 1.5 0.2 setosa
## 41 5.0 3.5 1.3 0.3 setosa
## 42 4.5 2.3 1.3 0.3 setosa
## 43 4.4 3.2 1.3 0.2 setosa
## 44 5.0 3.5 1.6 0.6 setosa
## 45 5.1 3.8 1.9 0.4 setosa
## 46 4.8 3.0 1.4 0.3 setosa
## 47 5.1 3.8 1.6 0.2 setosa
## 48 4.6 3.2 1.4 0.2 setosa
## 49 5.3 3.7 1.5 0.2 setosa
## 50 5.0 3.3 1.4 0.2 setosadat[dat$Species=="setosa",c(2,3,4,5)]## Sepal.Width Petal.Length Petal.Width Species
## 1 3.5 1.4 0.2 setosa
## 2 3.0 1.4 0.2 setosa
## 3 3.2 1.3 0.2 setosa
## 4 3.1 1.5 0.2 setosa
## 5 3.6 1.4 0.2 setosa
## 6 3.9 1.7 0.4 setosa
## 7 3.4 1.4 0.3 setosa
## 8 3.4 1.5 0.2 setosa
## 9 2.9 1.4 0.2 setosa
## 10 3.1 1.5 0.1 setosa
## 11 3.7 1.5 0.2 setosa
## 12 3.4 1.6 0.2 setosa
## 13 3.0 1.4 0.1 setosa
## 14 3.0 1.1 0.1 setosa
## 15 4.0 1.2 0.2 setosa
## 16 4.4 1.5 0.4 setosa
## 17 3.9 1.3 0.4 setosa
## 18 3.5 1.4 0.3 setosa
## 19 3.8 1.7 0.3 setosa
## 20 3.8 1.5 0.3 setosa
## 21 3.4 1.7 0.2 setosa
## 22 3.7 1.5 0.4 setosa
## 23 3.6 1.0 0.2 setosa
## 24 3.3 1.7 0.5 setosa
## 25 3.4 1.9 0.2 setosa
## 26 3.0 1.6 0.2 setosa
## 27 3.4 1.6 0.4 setosa
## 28 3.5 1.5 0.2 setosa
## 29 3.4 1.4 0.2 setosa
## 30 3.2 1.6 0.2 setosa
## 31 3.1 1.6 0.2 setosa
## 32 3.4 1.5 0.4 setosa
## 33 4.1 1.5 0.1 setosa
## 34 4.2 1.4 0.2 setosa
## 35 3.1 1.5 0.2 setosa
## 36 3.2 1.2 0.2 setosa
## 37 3.5 1.3 0.2 setosa
## 38 3.6 1.4 0.1 setosa
## 39 3.0 1.3 0.2 setosa
## 40 3.4 1.5 0.2 setosa
## 41 3.5 1.3 0.3 setosa
## 42 2.3 1.3 0.3 setosa
## 43 3.2 1.3 0.2 setosa
## 44 3.5 1.6 0.6 setosa
## 45 3.8 1.9 0.4 setosa
## 46 3.0 1.4 0.3 setosa
## 47 3.8 1.6 0.2 setosa
## 48 3.2 1.4 0.2 setosa
## 49 3.7 1.5 0.2 setosa
## 50 3.3 1.4 0.2 setosa##equivalent to:
dat[dat$Species=="setosa",-1]## Sepal.Width Petal.Length Petal.Width Species
## 1 3.5 1.4 0.2 setosa
## 2 3.0 1.4 0.2 setosa
## 3 3.2 1.3 0.2 setosa
## 4 3.1 1.5 0.2 setosa
## 5 3.6 1.4 0.2 setosa
## 6 3.9 1.7 0.4 setosa
## 7 3.4 1.4 0.3 setosa
## 8 3.4 1.5 0.2 setosa
## 9 2.9 1.4 0.2 setosa
## 10 3.1 1.5 0.1 setosa
## 11 3.7 1.5 0.2 setosa
## 12 3.4 1.6 0.2 setosa
## 13 3.0 1.4 0.1 setosa
## 14 3.0 1.1 0.1 setosa
## 15 4.0 1.2 0.2 setosa
## 16 4.4 1.5 0.4 setosa
## 17 3.9 1.3 0.4 setosa
## 18 3.5 1.4 0.3 setosa
## 19 3.8 1.7 0.3 setosa
## 20 3.8 1.5 0.3 setosa
## 21 3.4 1.7 0.2 setosa
## 22 3.7 1.5 0.4 setosa
## 23 3.6 1.0 0.2 setosa
## 24 3.3 1.7 0.5 setosa
## 25 3.4 1.9 0.2 setosa
## 26 3.0 1.6 0.2 setosa
## 27 3.4 1.6 0.4 setosa
## 28 3.5 1.5 0.2 setosa
## 29 3.4 1.4 0.2 setosa
## 30 3.2 1.6 0.2 setosa
## 31 3.1 1.6 0.2 setosa
## 32 3.4 1.5 0.4 setosa
## 33 4.1 1.5 0.1 setosa
## 34 4.2 1.4 0.2 setosa
## 35 3.1 1.5 0.2 setosa
## 36 3.2 1.2 0.2 setosa
## 37 3.5 1.3 0.2 setosa
## 38 3.6 1.4 0.1 setosa
## 39 3.0 1.3 0.2 setosa
## 40 3.4 1.5 0.2 setosa
## 41 3.5 1.3 0.3 setosa
## 42 2.3 1.3 0.3 setosa
## 43 3.2 1.3 0.2 setosa
## 44 3.5 1.6 0.6 setosa
## 45 3.8 1.9 0.4 setosa
## 46 3.0 1.4 0.3 setosa
## 47 3.8 1.6 0.2 setosa
## 48 3.2 1.4 0.2 setosa
## 49 3.7 1.5 0.2 setosa
## 50 3.3 1.4 0.2 setosa##also equivalent to:
setosaCol2through5 <- dat[dat$Species=="setosa",c(2:5)]
write.csv(setosaCol2through5, file = "~/Downloads/myFirstFile.csv", row.names = FALSE)
dat[4,1]## [1] 4.6#if you want to subset columns 3 and 4:
dat[,c(3,4)]## Petal.Length Petal.Width
## 1 1.4 0.2
## 2 1.4 0.2
## 3 1.3 0.2
## 4 1.5 0.2
## 5 1.4 0.2
## 6 1.7 0.4
## 7 1.4 0.3
## 8 1.5 0.2
## 9 1.4 0.2
## 10 1.5 0.1
## 11 1.5 0.2
## 12 1.6 0.2
## 13 1.4 0.1
## 14 1.1 0.1
## 15 1.2 0.2
## 16 1.5 0.4
## 17 1.3 0.4
## 18 1.4 0.3
## 19 1.7 0.3
## 20 1.5 0.3
## 21 1.7 0.2
## 22 1.5 0.4
## 23 1.0 0.2
## 24 1.7 0.5
## 25 1.9 0.2
## 26 1.6 0.2
## 27 1.6 0.4
## 28 1.5 0.2
## 29 1.4 0.2
## 30 1.6 0.2
## 31 1.6 0.2
## 32 1.5 0.4
## 33 1.5 0.1
## 34 1.4 0.2
## 35 1.5 0.2
## 36 1.2 0.2
## 37 1.3 0.2
## 38 1.4 0.1
## 39 1.3 0.2
## 40 1.5 0.2
## 41 1.3 0.3
## 42 1.3 0.3
## 43 1.3 0.2
## 44 1.6 0.6
## 45 1.9 0.4
## 46 1.4 0.3
## 47 1.6 0.2
## 48 1.4 0.2
## 49 1.5 0.2
## 50 1.4 0.2
## 51 4.7 1.4
## 52 4.5 1.5
## 53 4.9 1.5
## 54 4.0 1.3
## 55 4.6 1.5
## 56 4.5 1.3
## 57 4.7 1.6
## 58 3.3 1.0
## 59 4.6 1.3
## 60 3.9 1.4
## 61 3.5 1.0
## 62 4.2 1.5
## 63 4.0 1.0
## 64 4.7 1.4
## 65 3.6 1.3
## 66 4.4 1.4
## 67 4.5 1.5
## 68 4.1 1.0
## 69 4.5 1.5
## 70 3.9 1.1
## 71 4.8 1.8
## 72 4.0 1.3
## 73 4.9 1.5
## 74 4.7 1.2
## 75 4.3 1.3
## 76 4.4 1.4
## 77 4.8 1.4
## 78 5.0 1.7
## 79 4.5 1.5
## 80 3.5 1.0
## 81 3.8 1.1
## 82 3.7 1.0
## 83 3.9 1.2
## 84 5.1 1.6
## 85 4.5 1.5
## 86 4.5 1.6
## 87 4.7 1.5
## 88 4.4 1.3
## 89 4.1 1.3
## 90 4.0 1.3
## 91 4.4 1.2
## 92 4.6 1.4
## 93 4.0 1.2
## 94 3.3 1.0
## 95 4.2 1.3
## 96 4.2 1.2
## 97 4.2 1.3
## 98 4.3 1.3
## 99 3.0 1.1
## 100 4.1 1.3
## 101 6.0 2.5
## 102 5.1 1.9
## 103 5.9 2.1
## 104 5.6 1.8
## 105 5.8 2.2
## 106 6.6 2.1
## 107 4.5 1.7
## 108 6.3 1.8
## 109 5.8 1.8
## 110 6.1 2.5
## 111 5.1 2.0
## 112 5.3 1.9
## 113 5.5 2.1
## 114 5.0 2.0
## 115 5.1 2.4
## 116 5.3 2.3
## 117 5.5 1.8
## 118 6.7 2.2
## 119 6.9 2.3
## 120 5.0 1.5
## 121 5.7 2.3
## 122 4.9 2.0
## 123 6.7 2.0
## 124 4.9 1.8
## 125 5.7 2.1
## 126 6.0 1.8
## 127 4.8 1.8
## 128 4.9 1.8
## 129 5.6 2.1
## 130 5.8 1.6
## 131 6.1 1.9
## 132 6.4 2.0
## 133 5.6 2.2
## 134 5.1 1.5
## 135 5.6 1.4
## 136 6.1 2.3
## 137 5.6 2.4
## 138 5.5 1.8
## 139 4.8 1.8
## 140 5.4 2.1
## 141 5.6 2.4
## 142 5.1 2.3
## 143 5.1 1.9
## 144 5.9 2.3
## 145 5.7 2.5
## 146 5.2 2.3
## 147 5.0 1.9
## 148 5.2 2.0
## 149 5.4 2.3
## 150 5.1 1.8#if you want to subset raws 4 and 6:
dat[c(4,6),]## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 4 4.6 3.1 1.5 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa## When you are subsetting a vector, which is a 1-D object, you only need the index of the item you are subsetting. No comma because you do not need row and column indices. For example:
myVector <- LETTERS[1:10] ## LETTERS and letters are base constants in R for the 26 letters of the alphabet in either upper- or lower-case.
myVector## [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J"myVector[3] ## subset the 3rd element in this vector## [1] "C"## Let's subset just the rows that correspond to setosa in the dat dataset:
dat$Petal.Length[dat$Species=="setosa"]##here we use a conditional statement (dat$Species=="setosa" returns a vector of TRUE's and FALSE's) to tell R which element of the Petal.Length vector we want to subset## [1] 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 1.5 1.6 1.4 1.1 1.2 1.5 1.3
## [18] 1.4 1.7 1.5 1.7 1.5 1.0 1.7 1.9 1.6 1.6 1.5 1.4 1.6 1.6 1.5 1.5 1.4
## [35] 1.5 1.2 1.3 1.4 1.3 1.5 1.3 1.3 1.3 1.6 1.9 1.4 1.6 1.4 1.5 1.4#Just type this if you're not sure you understand
dat$Species=="setosa"## [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [12] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [23] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [34] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [45] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
## [56] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [67] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [78] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [89] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [100] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [111] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [122] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [144] FALSE FALSE FALSE FALSE FALSE FALSE FALSEGraphical options: a few examples
Let’s try to plot a basic graph again. Pay attention to the arguments used below.
plot(dat$Petal.Length, dat$Sepal.Length,
main="my nice title", ## main plot title
sub="blah", ## a subtitle for the plot
bty="l", ## box type for the plot
xlab="Iris petal length", ## x-axis label
ylab="Iris sepal length", ## y-axis label
xlim=c(0,7), ylim=c(0,8), ## limits for x and y axes
pch=6, ## character type for points
cex=0.5, ## size of plot points
## col=dat$Species ## this will set colors 1:3 for each species
col=ifelse(dat$Species=="setosa", "red", ifelse(dat$Species=="versicolor", "blue", "green")) ## you can also use numbers for basic colors such as 1,2,3, etc.
## the nested ifelse function above let's you set the color for points based on a series statements
)
## Note about creating a numeric vector:
c(1,2,3,4, 5, 6, 7, 8, 9, 10, 11)## [1] 1 2 3 4 5 6 7 8 9 10 11## is equivalent to
1:11 ## this is useful if you have a long list of consecutive numbers## [1] 1 2 3 4 5 6 7 8 9 10 11## Take a quick look at what all the plotting characters look like.
plot(1:20, 1:20, pch=1:20, cex=1.2, main="Different plotting characters in R", xlab=NA, ylab=NA) ## if you want to remove the axis titles, you can assign the axis titles as NA
##look at this one too:
plot(x = 1:10, y=10:1, bty="l", cex=2, cex.axis=1.5, main="lame graph", cex.main=.5, fg="red", col.lab="blue", col.main="yellow", col.axis="purple", family="Georgia")
## histogram:
myHist <- hist(dat$Petal.Length, col="darkmagenta", main="histogram of something", xlab="Petal length", ylab="counts", nclass=50)
barplot(myHist$counts, horiz=TRUE)
myHist <- hist(dat$Petal.Length, col="darkmagenta", main="histogram of something", xlab="Petal length", ylab="counts", nclass=20, las=1)
Interactive graphs
There are many packages available to create interactive graphs. Plotly is a good start.
##interactive graph
install.packages("plotly")##only the first time you use package "plotly" with yout computerlibrary(plotly)
p <- plot_ly(x = dat$Sepal.Length, y = dat$Petal.Length)
p