## Objectives

There are no example plots here. These notes are to assist in understanding some key options in the functions as used in R. See Module 6 Plotting in R for examples.

- To explain option in basic plots (plot, hist, boxplot)
- How to position plots on a page
- Explaining options in package lattice
- Explaining options for ggplot from library(ggplot2)

Back to Top

You need to know your data. For instance you need to know the variable names (R is case sensitive), and you may need the range of data. Use the functions names() and summary() to get this information. You also need to be aware of the type of data, is your variable a numeric or a factor?

## 1. To explain options in basic plots (plot, hist, boxplot)

To follow this code let:

dat be the dataset,

var2, var2 be a continuous variables and

grp1, grp2 be the grouping/categorical variables

`hist(var, breaks=c(5,10,15,20)) # the breaks option determines the cut points for the histogram`

A density plot: `dens(var) or `

` hist(var,freq=FALSE)`

If you assign the histogram to an object you can then add lines to it:

`myhist < - hist(var,freq=FALSE)`

` lines(myhist)`

To make a boxplot:

`boxplot(var~grp, data=dat)`

This gives a box and whisker plot. The default whiskers are extended to the max and min of the data or 1.5 times the IQR, whichever is the smaller.

To ensure they do cover the range you can change the range option:

`boxplot(var~ grp, data=dat, range=0)`

Plotting a scatterplot, with two continuous variables, as two columns in the dataset

^{?}View Code RSPLUS

**Type of plot**, for a line type=’l’, for a points type=’p”, and for both type=’b’.

**Changing colours of points**, use option col=”red”, “blue”, “purple”,

To get a list of colours use colours()

**Changing point type**, use pch=19 through to pch=25

**Adding lines**, after applying a regression model, fitted lines can be added.See Module 3 Regression

The plot() function is quite powerful in R. The type of plot you get depends on the R object it is applied to.

Note if the object is a dataset, or a model it will give different plots. The defaults for particular object types are considered the sensible option, or useful for that object.

Back to top

## 2. How to position plots on a page

When plotting, we need to use a function to help us place the plot on a page. The default is one plot on the page, but if we wish to change this we need to save the original graphics setting.

The code here saves the original setting, then plots 2 side by side and then replaces the original page setting.

^{?}View Code RSPLUS

So to get

- side by side plots use par(mfrow=c(1,2)),
- to have one above the other use par(mfcol=c(1,2)), and
- to get 4 per page par(mfrow=c(2,2))

## 3 Explaining options in lattice plots

The package lattice allows the plotting of facets of the data, here we have a plot of var1 versus grp1 with facets for each of the second grp2. This plotting function uses the formula code for the plot.

^{?}View Code RSPLUS

In some cases you may need to ensure the **grouping variable is a factor**.

This can be also added in the code

`xyplot(var~grp | factor(grp2), data=dat)`

**To add trend lines for regression**

```
xyplot(var~grp | factor(grp2), data=dat,
type=c("p", "r"))
```

**To add a plot title and axis title**

^{?}View Code RSPLUS

xyplot(var~grp | factor(grp2), data=dat, type=c("p", "r"), main ="My first Lattice plot", ylab ="Y axis label", xlab ="X axis label" ) |

**To change font size in titles and on the scale**

^{?}View Code RSPLUS

xyplot(var~grp | factor(grp2), data=dat, type=c("p", "r"), main =list ( label ="My first Lattice plot", cex=0.75) ylab =list ( label ="Y axis label", cex=0.75) xlab =list ( label ="X axis label", cex=0.75), scales =list(cex=0.5)) |

**Other types of plot available in library(lattice) are:**

Bar charts barchart()

Box and Whisker plot bwplot()

One dimensional strip plot stripplot()

Three dimensional plots cloud()

Three dimensional surface plots wireframe()

**Using the Help features**

Once you come familiar use the R HELP and the package lattice help and documentation.

Back to top

## 4. Explaining options for ggplot from library(ggplot2)

This package has its own way of specifying the data and the plot. Some examples are given in Module 6.

The function is ggplot() but it is from library(ggplot2).

^{?}View Code RSPLUS

mygplot < - ggplot(dat, aes(x=xvar, y=yvar) + geom_point() + stat_smooth()) |

There are specifications for **aesthetics**, defining the variables and the **geom or stat **to define the style of plot, and finally the line style with **stat**.

ggplot2 | Comment |
---|---|

Requires data in a data frame | Define the data set. It must be a data frame |

Mapping data to the plot aes (aesthetics) | aes(x=xvar, y= yar) This maps the data to the visual elements in the plot (aesthetics) |

Terminology geom object or a stat object. How to display the data | geom_bar() geom_histogram bar chart. You can specify binwidth |

geom_point() scatterplot | |

geom_line() line connecting observations in x order | |

geom_boxplot() box and whisker | |

geom_smooth() smooth conditioned mean | |

geom_path() connecting observations in original order | |

Terminology for stat | stat_bin() bar chart |

stat_identity() scatter or line plot | |

stat_boxplot() | |

stat_identity() connecting observations in original order | |

Stat_smooth() smooth conditioned mean . Choose method=lm to add a regression, or method=loess | |

Axis title control | use xlab and ylab |

For Main title | opts(title=”Overall plot title”) |

Other features | Facet- grid to make a row and column array of plots, scales, colour, |

See also the main plotting Module 6 for selected examples

Please contact us and ask for particular plots you would like explained.

Back to top

## Recent Comments