1. R-Graphics Stephen Opiyo

2. Basic Graphs One of the main reasons data analysts turn to R is for its strong graphic capabilities. R generates publication-ready figures. "graphics" library loads by default when R is started. Ready to go as soon as R opens. 2

3. Graphing basics Plotting commands 1.High-level functions: Create a new plot on the graphics device 2.Low-level functions: Add more information to an already existing plot, such as extra points, lines, and labels 3

4. Common high-level functions plot(): A generic function that produces a type of plot that is dependent on the type of the first argument. hist(): Creates a histogram of frequencies barplot(): Creates a histogram of values boxplot(): Creates a boxplot 4

5. Example 1 Download data D2_Data_1 Open file D2_Example_1.R R dataset mtcars 5

6. Lower level graphical functions pch (plotting characters)=“ ” : character or numbers col (color) = “ ” : character or numbers lty = numbers lwd = numbers axes = “L”: L= F, T xlab =“string”, ylab=“string” sub = “string”, main =“string” xlim = c(lo,hi), ylim= c(lo,hi) cex controls the symbol size in the plot, default is cex=1, 6

7. plot type description: type= " " p= points l =lines o= over plotted points and lines b, c= points (empty if "c") joined by lines s= stair steps h= histogram-like vertical lines n = does not produce any points or lines Lower level graphical functions 7

8. Lower-level graphing functions pch=0,square pch=1,circle pch=2,triangle point up pch=3,plus pch=4,cross pch=5,diamond pch=6,triangle point down pch=7,square cross pch=8,star pch=9,diamond plus pch=10,circle plus pch=11,triangles up and down pch=12,square plus pch=13,circle cross pch=14,square and triangle down pch=15, filled square blue pch=16, filled circle blue pch=17, filled triangle point up blue pch=18, filled diamond blue pch=19,solid circle blue pch=20,bullet (smaller circle) pch=21, filled circle red pch=22, filled square red pch=23, filled diamond red pch=24, filled triangle point up red pch=25, triangle point down red 8

9. Lower-level graphing functions Symbol shapes and colors 9

10. Lower-level graphing functions Adding text text() text(x,y, “text”, options) points() add some more points to the graph points(x,y, options) Saving graphs in Rstudio 10

11. Example 2 Download data D2_Data_2 Open file D2_Example_2.R 11

12. Making a histogram Make histograms with varying the number of bars (also called ‘bins’ or ‘cells’), e.g. simdata <-rchisq(100,8) hist(simdata) # default number of bins Setting your own breakpoints bps <- c(0,2,4,6,8,10,15,25) hist(simdata,breaks=bps) 12

13. 3-dimensional Scatterplots Need a package scatterplot3d Install package scatterplot3d using install.packages("scatterplot3d") command Alternatively install using Rstudio using Packages 13

14. Multiple graph on one page Combining multiple plots using par () and mfrow = c(nrows, ncols) to create a matrix of nrows by ncols ?par par(mfrow=c(1,2)) 14

15. Exercise 15 par(mfrow=c(3,5)) plot(D2_Data_2[,2], D2_Data_2[,3], type="p", pch=1, col="1", xlab ="Peak1", ylab ="Peak2", main="Plot of Peak1 vs Peak2", font.main =1) Replace pch=1 and col =1 with 2 to 15: Export the graph and save it as Day_2_Graph.pdf