{"id":228,"date":"2010-05-04T18:25:21","date_gmt":"2010-05-04T22:25:21","guid":{"rendered":"http:\/\/lukemiller.org\/?p=228"},"modified":"2011-05-10T16:48:52","modified_gmt":"2011-05-10T20:48:52","slug":"modifying-basic-plots-in-r","status":"publish","type":"post","link":"https:\/\/lukemiller.org\/index.php\/2010\/05\/modifying-basic-plots-in-r\/","title":{"rendered":"Modifying basic plots in R"},"content":{"rendered":"

Below is a walk-through of some of the basics of customizing plots in R. These are all based on the graphics<\/code> package that comes in the base installation of R.<\/p>\n

Let’s start by making a basic plot in R. In the code snippets below, green text behind a # sign is considered comments by R, so everything after a # sign on a line will be ignored by R. We’ll call the plot<\/code> command and supply it with two vectors of numbers representing the x and y values:
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1)) #x and y data for our example plot<\/span>
\n<\/code>
\nwhich produces this plot:<\/p>\n

\"\"
The basic plot.<\/figcaption><\/figure>\n

\"\"<\/p>\n

 <\/p>\n

The basic plot isn’t the most attractive thing in the world. We can start prettying it up by adjusting the graphical parameters of the plot. This is most easily done by inserting parameter definitions into the plot command.<\/p>\n

We’ll start by adding labels to the x and y axes, along with a plot title. Note the commas at the end of each line, they are important. Newly inserted code is highlighted in red:
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\",<\/span> #X axis title<\/span>
\nylab = \"Sample value\",<\/span> #Y axis title<\/span>
\nmain = \"Test\",<\/span> #Main title of plot<\/span>
\n)\t\t\t #Closing parenthesis for plot command<\/span>
\n<\/code>
\nwhich makes the following plot:<\/p>\n

\"\"
Now with axis labels and a title. <\/figcaption><\/figure>\n

\"\"<\/p>\n

 <\/p>\n

One thing that bugs me about the basic R plot is that the y-axis tick labels are rotated
\nto a vertical orientation. I don’t think that it’s ever advisable to make a plot
\nharder<\/em> to read, so I like my y-axis labels horizontal. We can add one more line to
\nthe plot command to make the tick labels horizontal:
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", \t\t #Main title of plot<\/span>
\nlas = 1,<\/span> #Rotate all tick labels horizontal<\/span>
\n)\t\t\t #Closing parenthesis for plot command
\n<\/span> <\/code>
\nwhich makes this plot:<\/p>\n

\"\"
Note the y-axis tick labels are now horizontal.<\/figcaption><\/figure>\n

The las<\/code> parameter has 4 possible values: 0 = parallel to axis, 1 = all horizontal, 2 =
\nperpendicular to axis, 3 = all vertical. When we modify the las<\/code> parameter in the plot
\ncommand, it applies to the tick labels on both the x and y axes at the same time.
\n\"\"
\nNow we can start going hog-wild and changing other parameters to further modify the plot.
\nLet’s make this plot have lines between the points by setting the type<\/code> parameter, and
\nlet’s make those lines dotted using the lty<\/code> parameter.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", \t\t #Main title of plot<\/span>
\nlas = 1,\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",<\/span> #Plot points with lines between them.<\/span>
\nlty = 3,<\/span> #Define line type. 0 = blank, 3 = dotted<\/span>
\n)\t\t\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
The points are now connected by a dotted line.<\/figcaption><\/figure>\n

\"\"
\nThe font style and size can be modified as well. The following command will use
\nfont.axis<\/code> to change the axis tick labels to bold italics, and font.main<\/code> to change the
\nmain title to italics. Why would you ever do this? I’m not sure.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", \t\t #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",\t #Plot points with lines between them.<\/span>
\nlty = 3,\t\t #Define line type. 0 = blank, 3 = dotted<\/span>
\nfont.axis = 4,<\/span> #Display axis tick labels in bold italics<\/span>
\nfont.main = 3,<\/span> #Display the main title in italics<\/span>
\n)\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
The tick labels are in italics for some reason.<\/figcaption><\/figure>\n

\"\"
\nNext let’s try making the axis tick labels larger using cex.axis<\/code> and make
\nthe main title larger using cex.main<\/code>.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",\t\t #Plot points with lines between them.<\/span>
\nlty = 3,\t #Define line type. 0 = blank, 3 = dotted<\/span>
\nfont.axis = 4,\t\t #Display axis tick labels in bold italics<\/span>
\nfont.main = 3,\t\t #Display the main title in italics<\/span>
\ncex.axis = 1.2,<\/span> #Make axis tick labels 1.2x larger than regular font<\/span>
\ncex.main = 1.5,<\/span> #Make main title 1.5x larger than regular font size<\/span>
\n)\t\t\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
The labels have gotten larger.<\/figcaption><\/figure>\n

\"\"
\nWe can also make the axis titles larger using the cex.lab<\/code> parameter:
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", \t\t #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",\t\t #Plot points with lines between them.<\/span>
\nlty = 3,\t #Define line type. 0 = blank, 3 = dotted<\/span>
\nfont.axis = 4,\t #Display axis tick labels in bold italics<\/span>
\nfont.main = 3,\t #Display the main title in italics<\/span>
\ncex.axis = 1.2,\t #Make axis tick labels 1.2x larger than regular font<\/span>
\ncex.main = 1.5,\t \t #Make main title 1.5x larger than regular font size<\/span>
\ncex.lab = 1.5,<\/span> #Make axis title 1.5x larger than regular font size<\/span>
\n)\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
Even the axis titles are larger.<\/figcaption><\/figure>\n

\"\"
\nMaybe the journal you’re submitting to doesn’t like figures to be enclosed in a box. The
\naxes that are displayed can be modified with the bty<\/code> parameter. Here we’ll remove the
\ntop and right side axes.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", \t\t #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",\t\t #Plot points with lines between them.<\/span>
\nlty = 3,\t #Define line type. 0 = blank, 3 = dotted<\/span>
\nfont.axis = 4,\t #Display axis tick labels in bold italics<\/span>
\nfont.main = 3,\t\t #Display the main title in italics<\/span>
\ncex.axis = 1.2,\t #Make axis tick labels 1.2x larger than regular font<\/span>
\ncex.main = 1.5,\t #Make main title 1.5x larger than regular font size<\/span>
\ncex.lab = 1.5,\t\t #Make axis title 1.5x larger than regular font size<\/span>
\nbty = \"l\", <\/span> #Specify which axes to draw (l = left + bottom)<\/span>
\n)\t\t\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
The upper and right sides of the plot box are now gone.<\/figcaption><\/figure>\n

\"\"
\nPerhaps you want to squeeze the axes titles in a bit closer to the actual plot. This can
\nbe accomplished with the mgp<\/code> parameter, which also affects the location of the axis
\ntick labels and the actual ticks. You supply mgp<\/code> with a 3-value vector, where the 1st
\nvalue is the location of the axis title, the 2nd value is the tick label location, and
\nthe 3rd value is the tick location. We’ll move the axis titles in slightly here.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", #Main title of plot<\/span>
\nlas = 1,\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",\t #Plot points with lines between them.<\/span>
\nlty = 3,\t #Define line type. 0 = blank, 3 = dotted<\/span>
\nfont.axis = 4,\t #Display axis tick labels in bold italics<\/span>
\nfont.main = 3,\t #Display the main title in italics<\/span>
\ncex.axis = 1.2,\t\t #Make axis tick labels 1.2x larger than regular font<\/span>
\ncex.main = 1.5,\t #Make main title 1.5x larger than regular font size<\/span>
\ncex.lab = 1.5,\t\t #Make axis title 1.5x larger than regular font size<\/span>
\nbty = \"l\",\t\t #Specify which axes to draw (l = left + bottom)<\/span>
\nmgp = c(2.1,1,0),<\/span> #Specify axis label + tick locations relative to plot<\/span>
\n)\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
The axis titles have shifted closer to the axes.<\/figcaption><\/figure>\n

\"\"
\nNext let’s add some color to the plot (it’s going to get ugly really quick). The various
\ncol<\/code> parameters modify the colors of the plot components. If you want to know all of the
\ncolors you can refer to by name, type colors()<\/code> at the R command prompt.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = \"Sample value\", #Y axis title<\/span>
\nmain = \"Test\", \t\t #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\ntype = \"b\",\t #Plot points with lines between them.<\/span>
\nlty = 3,\t\t #Define line type. 0 = blank, 3 = dotted<\/span>
\nfont.axis = 4,\t #Display axis tick labels in bold italics<\/span>
\nfont.main = 3,\t\t #Display the main title in italics<\/span>
\ncex.axis = 1.2,\t #Make axis tick labels 1.2x larger than regular font<\/span>
\ncex.main = 1.5,\t \t #Make main title 1.5x larger than regular font size<\/span>
\ncex.lab = 1.5,\t #Make axis title 1.5x larger than regular font size<\/span>
\nbty = \"l\",\t #Specify which axes to draw (l = left + bottom)<\/span>
\nmgp = c(2.1,1,0),\t #Specify axis label + tick locations relative to plot<\/span>
\ncol = \"red\",<\/span> #Plot the points + lines in red<\/span>
\ncol.axis = \"blue\",<\/span> #Set the axis tick label color<\/span>
\ncol.lab = \"dark red\",<\/span> #Set the axis title color<\/span>
\ncol.main = \"#CC00CC\",<\/span> #Set the figure title color using hex values.<\/span>
\n#Hex values are simply an alternate way to specify a
\n#color.<\/span>
\n)\t\t\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
Those are some horrible colors.<\/figcaption><\/figure>\n

There are lots of other parameters you can modify in your figure. You can find out about
\nall the other parameters by typing ? par<\/code> at the R command prompt.
\n\"\"<\/p>\n

One of the other things you might want to do is insert special characters in the axis
\ntitles. For instance, maybe the units of our y-axis are actually degrees Celsius. Getting
\na degree symbol is slightly more involved, but here’s one way to do it:
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = expression(paste(\"Temp, \",degree,\"C\")),<\/span> #Y axis title<\/span>
\nmain = \"Test\", #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\n)\t #Closing parenthesis for plot command<\/span>
\n<\/code><\/p>\n

\"\"
The y-axis label now has a fancy degree sign in it.<\/figcaption><\/figure>\n

In the code above, the ylab = expression(paste(\"Temp, \",degree,\"C\")),<\/code> is doing something exciting. Using expression<\/code> tells R to evaluate the code inside the parentheses. Inside those parentheses, we have a paste<\/code> command, which tells R to stick the items inside paste’s parentheses together in a string. This combination of commands instructs R to create a string, but evaluate any special code words first. In this case, the code word is degree<\/code>, which R turns into a degree symbol and sticks in between the \"Temp, \"<\/code> and \"C\"<\/code> strings.
\n\"\"<\/p>\n

There may also be instances where you want one of your axes to have different fonts,
\ncolors, size etc. This is accomplished by first suppressing the text for that axis in the
\nplot command using the yaxt<\/code> or xaxt<\/code> parameters, and then using a subsequent command
\nlike axis<\/code> to modify the desired axis. In the example below, we’re going to suppress the
\ny-axis using the yaxt = \"n\"<\/code> parameter inside the plot command. Then we’ll
\nfollow the plot command with the axis<\/code> command wherein we lay out the parameters of the
\ny-axis. When the plot command is called, R still calculates where to put the y-axis
\nlabels and what their values should be, and it holds these in memory so that you can use
\nthem with the axis<\/code> command.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = expression(paste(\"Temp, \",degree,\"C\")), #Y axis title<\/span>
\nmain = \"Test\", #Main title of plot<\/span>
\nlas = 1,\t #Rotate all tick labels horizontal<\/span>
\nyaxt = \"n\",<\/span> #Suppress y-axis tick labels and title<\/span>
\n)\t #Closing parenthesis for plot command<\/span>
\n<\/code>
\naxis(2,<\/span> #Define which axis to modify. 1 = bottom x-axis, 2 = left y-axis, 3 = top etc...<\/span>
\nlas = 1,<\/span> #Set tick label orientation (1 = horizontal)<\/span>
\ncex.axis = 0.8,<\/span> #Set font size (0.8 times current font size)<\/span>
\nfont.axis = 3,<\/span> #Set font style (bold,italics etc, 3 = italics)<\/span>
\ncol.axis = \"tan4\",<\/span> #Set axis color<\/span>
\n)<\/span> #Closing parenthesis for axis command<\/span>
\n<\/code><\/p>\n

\"\"
The format of the y-axis tick labels is different than the x-axis tick labels.<\/figcaption><\/figure>\n

\"\"<\/p>\n

 <\/p>\n

Finally, you can drop text notations on the plot using the text<\/code> command and specifying
\nthe x,y location of the text. Again we’ll use a greek symbol here.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1), #x and y data for our example plot<\/span>
\nxlab = \"Sample number\", #X axis title<\/span>
\nylab = expression(paste(\"Temp, \",degree,\"C\")), #Y axis title<\/span>
\nmain = \"Test\", #Main title of plot<\/span>
\nlas = 1,\t\t #Rotate all tick labels horizontal<\/span>
\nyaxt = \"n\",\t #Suppress y-axis tick labels and title<\/span>
\n)\t #Closing parenthesis for plot command<\/span><\/code>
\n
\ntext(2,2,expression(paste(Delta,\"T\")))<\/span><\/code><\/p>\n

\"\"
Note the text label at (2,2) on the plot.<\/figcaption><\/figure>\n

\"\"<\/p>\n

 <\/p>\n

You can construct more elaborate labels using the facilities found in the R help for plotmath<\/code>. For example, we can construct a y-axis label with a combination of normal text, italics, a greek symbol, and some superscripts using the plain()<\/code> and italic()<\/code> functions (there are also bold and bolditalic options as well). In this case, we will construct the label before issuing the
\nplot command.<\/p>\n


\nmylab = expression(paste(plain('Final '),
\nitalic('per capita '),
\nplain('rate ('), #that is an opening parenthesis inside the quotes<\/span>
\nplain(mu), #greek symbols have special code words<\/span>
\nplain('g snail '^{-1}), #superscript goes outside the quotes<\/span>
\nplain('day'^{-1}),
\nplain(')') )) #there is a closing parenthesis in those quotes<\/span>
\n<\/code>
\nThe above command uses expression()<\/code> to create an expression object called mylab<\/code> that is stored in memory. Inside the expression()<\/code> command, we use paste()<\/code> to paste together several plain and italic text strings. Note that we surround per capita<\/em> with an italic()<\/code> command to italicize those words. The greek symbol mu is inserted by simply typing mu, without quote marks around it (similar to how we displayed the Delta symbol above). The superscript -1 symbols are written outside of quotes as well, but inside the plain()<\/code> parentheses. The use of the ^{ } symbols around the -1 tells R that we want everything inside the curly braces to be superscript (this is essentially TeX syntax, if you’re familiar with it). To make a subscript, you would use square braces [ ], and surround text with quotes inside the braces.<\/p>\n

After defining that mess of a label, we once again create our basic plot and instead of supplying a string for the ylab argument, we simply supply the expression stored in ‘mylab’ which is converted to text by R.
\n
\nplot(c(1,2,3,4,5,6),c(4,3,6,2,1,1),
\nxlab = 'Sample Number',
\nylab = mylab, #use mylab for the y-label. Do not put quotes around mylab.<\/span>
\nlas = 1,
\n)
\n<\/code><\/p>\n

\"\"<\/a>
The y-axis label contains a mix of plain and italics words, superscripts, and a greek symbol.<\/figcaption><\/figure>\n

\"\"
\nFor even more info on graphing in R and general R usage, I have found the Quick-R<\/a> site extremely informative. The sections on graphs<\/a> and advanced graphs<\/a> are quite helpful.<\/p>\n","protected":false},"excerpt":{"rendered":"

Below is a walk-through of some of the basics of customizing plots in R. These are all based on the graphics package that comes in the base installation of R. Let’s start by making a basic plot in R. In the code snippets below, green text behind a # sign is considered comments by R, […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[218],"tags":[82,16,85,17,7,58,84,83],"class_list":["post-228","post","type-post","status-publish","format-standard","hentry","category-r-project","tag-axis-label","tag-graphics","tag-greek-symbol","tag-plotting","tag-r","tag-r-project","tag-subscript","tag-superscript"],"_links":{"self":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts\/228","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/comments?post=228"}],"version-history":[{"count":75,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts\/228\/revisions"}],"predecessor-version":[{"id":304,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts\/228\/revisions\/304"}],"wp:attachment":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/media?parent=228"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/categories?post=228"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/tags?post=228"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}