1. R-Graphics Day 2 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 High-level functions Download data D2_Data_1 - metabolomics data with 10 peaks identified by Liquid Chromatography-Mass Spectrometer Open file D2_Example_1.R R has datasets with packages, e.g., mtcars - Will find out about the data from r using ?mtcars 5

6. 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 6

7. pch (plotting characters)=“ ” : character or numbers col (color) = “ ” : character or numbers lty (line type) = numbers lwd (line width) = numbers xlab (x label) =“string”, ylab (y label) =“string” main (heading) =“string” xlim (x limit) = c(lo,hi), ylim (y limit) = c(lo,hi) cex controls the symbol size in the plot, default is cex=1, 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 - metabolomics data with 4 peaks identified by Liquid Chromatography-Mass Spectrometer Open file D2_Example_2.R 11

12. 3-dimensional Scatterplots Need a package scatterplot3d Install package scatterplot3d using install.packages("scatterplot3d") command Alternatively install using Rstudio using Packages 12

13. 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)) 13

14. Exercise 1 14 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

15. Basic statistics using R Open file D2_Example_3.R - metabolomics data with 4 peaks identified by Liquid Chromatography-Mass Spectrometer Mean, standard deviation, median, mode Correlation Ttest 15

16. 1) Use R dataset called iris 2) What is the mean and standard deviation of Sepal.Length? 3) Find the correlation between Sepal.Length and Sepal.Width 4) Perform independent ttest between Petal.Length and Petal.Width 5) Test weather the mean of Sepal.Length is equal to 4 6) Find the median of Petal.Length 16 Exercise 2