The Base Plotting System in R Roger D. Peng, Associate Professor of Biostatistics Johns Hopkins Bloomberg School of Public HealthPlotting System The core plotting and graphics engine in R is encapsulated in the following packages: graphics: contains plotting functions for the "base" graphing systems, including plot, hist, boxplot and many others. grDevices: contains all the code implementing the various graphics devices, including X11, PDF, PostScript, PNG, etc. The lattice plotting system is implemented using the following packages: lattice: contains code for producing Trellis graphics, which are independent of the “base” graphics system; includes functions like xyplot, bwplot, levelplot grid: implements a different graphing system independent of the “base” system; the /attice package builds on top of grid; we seldom call functions from the grid package directly 210The Process of Making a Plot When making a plot one must first make a few considerations (not necessarily in this order) Where will the plot be made? On the screen? In a file? - How will the plot be used? Is the plot for viewing temporarily on the screen? Will it be presented in a web browser? Will it eventually end up in a paper that might be printed? Are you using it in a presentation? + Is there a large amount of data going into the plot? Or is it just a few points? + Do you need to be able to dynamically resize the graphic? 30The Process of Making a Plot - What graphics system will you use: base, lattice, or ggplot2? These generally cannot be mixed Base graphics are usually constructed piecemeal, with each aspect of the plot handled separately through a series of function calls; this is often conceptually simpler and allows plotting to mirror the thought process Lattice graphics are usually created in a single function call, so all of the graphics parameters have to specified at once; specifying everything at once allows R to automatically calculate the necessary spacings and font sizes. + ggplot2 combines concepts from both base and lattice graphics but uses an independent implementation We focus on using the base plotting system to create graphics on the screen device 4r20Base Graphics Base graphics are used most commonly and are a very powerful system for creating 2-D graphics. There are two phases to creating a base plot ~ Initializing a new plot = Annotating (adding to) an existing plot Calling plot(x, y) orhist(x) will launch a graphics device (if one is not already open) and draw a new plot on the device If the arguments to pot are not of some special class, then the default method for p1ot is called; this function has many arguments, letting you set the title, x axis label, y axis label, etc. + The base graphics system has many parameters that can set and tweaked; these parameters are documented in 2par; it wouldn't hurt to try to memorize this help page! 520Simple Base Graphics: Histogram Library (datasets) hist(airqualitysozone) ## Draw a new plot. Histogram of airqualityS0zone secusita0zeneSimple Base Graphics: Scatterplot Library (datasets) with(airquality, plot(Wind, Ozone))Simple Base Graphics: Boxplot Library (datasets) airquality <- transform(airquality, Month = factor (Month) ) boxplot (Ozone ~ Month, airquality, xlab = "Month", ylab = "ozone (ppb)") ozme sb)Some Important Base Graphics Parameters Many base plotting functions share a set of parameters. Here are a few key ones: pch: the plotting symbol (default is open circle) ty: the line type (default is solid line), can be dashed, dotted, etc. + lwd: the line width, specified as an integer multiple + col: the plotting color, specified as a number, string, or hex code; the colors() function gives you a vector of colors by name + x1ab: character string for the x-axis label + ylab: character string for the y-axis label sroSome Important Base Graphics Parameters The par() function is used to specify global graphics parameters that affect all plots in an R session. These parameters can be overridden when specified as arguments to specific plotting functions. + Las: the orientation of the axis labels on the plot + bg: the background color mar: the margin size + oma: the outer margin size (default is 0 for all sides) m£row: number of plots per row, column (plots are filled row-wise) + m£col1: number of plots per row, column (plots are filled column-wise) 10720Some Important Base Graphics Parameters Default values for global graphics parameters par("lty") ## (1) “solid” par("col") ## (1) "black" par("peh") 4120 #1) 1Some Important Base Graphics Parameters Default values for global graphics parameters par("bg") ‘## (1) “transparent” par("mar") #1) 8.141 42 20 par ("mérow") 42100 wy itBase Plotting Functions + plot: make a scatterplot, or other type of plot depending on the class of the object being plotted Lines: add lines to a plot, given a vector x values and a corresponding vector of y values (or a 2- column matrix); this function just connects the dots points: add points to a plot + text: add text labels to a plot using specified x, y coordinates + title: add annotations to x, y axis labels, title, subtitle, outer margin + mtext: add arbitrary text to the margins (inner or outer) of the plot + axis: adding axis ticks/labels 13720Base Plot with Annotation Library (datasets) with(airquality, plot(Wind, Ozone)) title(main = "ozone and Wind in New York City") # Add a title (Ozone and Wind in New York City ovone 14120Base Plot with Annotation with(airquality, plot (Wind, ozone, main = "ozone and Wind in New York city")) with(subset(airquality, Month = 5), points(Wind, Ozone, col = “blue")) (Ozone and Wind in New York City ‘ene 15120Base Plot with Annotation with(airquality, plot(Wind, Ozone, main = "Ozone and Wind in New York city", type = "n")) with(subset(airquality, Month = 5), points(Wind, Ozone, col = "blue")) with(subset(airquality, Month != 5), points(Wind, Ozone, col = “red")) Jegend("topright", pch = 1, col = ¢("blue", "red"), legend = c("May", "Other Months") (Ozone and Wind in New York City ovone 16720Base Plot with Regression Line with(airquality, plot(Wind, Ozone, main = "Ozone and Wind in New York City", peh = 20)) model <- Im(Ozone ~ Wind, airquality) abline(model, Iwd = 2) (Ozone and Wind in New York City 150 100 one 17720Multiple Base Plots par(mfrow = ¢(1, 2)) with(airquality, { plot(Wind, Ozone, main = "Ozone and Wind") plot(Solar.R, Ozone, main = “Ozone and Solar Radiation") » ozone and Wind ‘ozone and Solar Radiation o 8 6 of * 28 coo” 22 o, , @ BO]. eee i cdg"? ee : we se . . ee gg Poo” ° ge 2 ees Bo cgeses ge ° ey oe 8 P08 2880 8st Rg go n,? Pandy, PS Hs 9 So MHS Po. . SW org eg ae es 2 0” 5 ‘0 8 ~ om mm m0 m0 Wind Soin 18720Multiple Base Plots par(mfrow = c(1, 3), mar = e(4, 4, 2, 1), oma = c(0, 0, 2, 0)) with(airquality, { plot (Wind, Ozone, main = “Ozone and Wind") plot(Solar-R, Ozone, main = “ozone and Solar Radiation") plot (Temp, Ozone, main = “Ozone and Temperature") mtext("Ozone and Weather in New York City", outer = TRUE) » ‘Czane ana Weather in New Yor ty 19720Summary + Plots in the base plotting system are created by calling successive R functions to "build up" a plot Plotting occurs in two stages: - Creation of a plot - Annotation of a plot (adding lines, points, text, legends) + The base plotting system is very flexible and offers a high degree of control over plotting 20K20