Welcome back

to “Computing for Molecular Biology 1”

We learned how todo this

How did we do that?

Exploring all data

plot(birth)

Numeric v/s Numeric

plot(head ~ weight, data=birth)

Numeric v/s Factor

plot(weight ~ sex, data=birth)

Boxplot

Plotting a numeric value depending on a factor results in a boxplot

It is a graphical version of summary().

  • The center is the median
  • The box is between the first and third quartil (50% of cases)
  • The wiskers extend a prediction of 95% of cases
  • Points are outliers

Nicer boxplot

plot(weight ~ sex, data=birth, boxwex=0.2, notch=TRUE, col="grey")

Factor v/s Factor

birth$apgar5 <- as.factor(birth$apgar5)
plot(sex ~ apgar5, data=birth)

Factor v/s Numeric

plot(sex ~ weight, data=birth)

Saving graphics

Graphical Devices

By default all plot() commands work on a RStudio window

We can open a new device and redirect plot() output

Try this and check the Files window

pdf()
plot(sex ~ weight, data=birth)
dev.off()

Don’t forget to close the device!!

PDF, PNG, OMG!

There are many outpit devices

The most used are pdf() and png()

Try this and check the Files window

png()
plot(sex ~ weight, data=birth)
dev.off()

Don’t forget to close the device!!

What is the difference?

  • PNG is a bitmap format: a bidimensional array of pixels
    • other examples are JPG, TIFF, GIF
  • PDF is a vectorial format: a mathematical description
    • other example is SVG

The difference is seen when you zoom in

  • PDF is good to print in paper
  • PNG is better for screen and presentations

Multiple plots

Try this:

pdf()
plot(sex ~ weight, data=birth)
plot(weight ~ sex, data=birth, boxwex=0.2, notch=TRUE, col="grey")
plot(sex ~ apgar5, data=birth)
dev.off()

and look at the files.

What do you see?

Multiple plots

Now try this:

pdf(onefile=FALSE)
plot(sex ~ weight, data=birth)
plot(weight ~ sex, data=birth, boxwex=0.2, notch=TRUE, col="grey")
plot(sex ~ apgar5, data=birth)
dev.off()

and look at the files.

What do you see?

PDF options

pdf(file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"),
    width, height, onefile, family, title, fonts, version,
    paper, encoding, bg, fg, pointsize, pagecentre, colormodel,
    useDingbats, useKerning, fillOddEven, compress)
paper:
“a4”, “letter”, “legal”, “executive”, “special”, “default”. Defaults to “special”
width, height:
specified in inches. Used when paper is “special”
file:
filename of the output file. Will be overwritten

PNG options

png(filename = "Rplot%03d.png",
    width = 480, height = 480, units = "px", pointsize = 12,
     bg = "white",  res = NA, ..., type, antialias)
width, height:
figure size, in “units”
units:
Can be px (pixels, the default), in (inches), cm or mm.
res:
The nominal resolution, in pixels per inch (ppi). Default 72.
pointsize:
the default pointsize of plotted text
bg:
the initial background colour: can be “transparent”.

But ploting many times is boring…

Functions in R

Whenever we need to execute the same set of commands more than 2 times, it can be useful to define a function

The format is:

new.function <- function(options) {
    command
    command
    ....
    command
    return(value)
}

Example

three.plots <- function() {
  plot(sex ~ weight, data=birth)
  plot(weight ~ sex, data=birth, boxwex=0.2, notch=TRUE, col="grey")
  plot(sex ~ apgar5, data=birth)
}

Using it

Try this, line by line:

three.plots()
pdf(file="three-plots.pdf", onefile=TRUE)
three.plots()
dev.off()
pdf(file="three-plots.pdf", onefile=TRUE)
par(mfrow=c(3,1))
three.plots()
dev.off()

Using it again

Try this now, line by line:

par(mfrow=c(3,1))
three.plots()
png()
three.plots()
dev.off()
png()
par(mfrow=c(3,1))
three.plots()
dev.off()

Passing values to the function

What if we want the same plots for different data?

For example, let’s define

healthy <- subset(birth, apgar5=="8" | apgar5=="9")

(how else can we build the data frame healthy?)

How can we draw the same plots for this data?

New data

summary(healthy)
       id            birth           apgar5    sex         weight    
 Min.   : 4199   Min.   :1.000   9      :388   F:247   Min.   :1180  
 1st Qu.: 6023   1st Qu.:1.000   8      :233   M:374   1st Qu.:2980  
 Median : 7894   Median :1.000   1      :  0           Median :3250  
 Mean   : 7836   Mean   :1.667   2      :  0           Mean   :3255  
 3rd Qu.: 9601   3rd Qu.:2.000   3      :  0           3rd Qu.:3570  
 Max.   :11475   Max.   :3.000   4      :  0           Max.   :5000  
                                 (Other):  0                         
      head            age            parity          weeks      
 Min.   :35.50   Min.   :22.00   Min.   :1.000   Min.   :29.00  
 1st Qu.:48.00   1st Qu.:33.50   1st Qu.:1.000   1st Qu.:38.00  
 Median :49.50   Median :34.50   Median :2.000   Median :39.00  
 Mean   :49.37   Mean   :34.45   Mean   :2.599   Mean   :38.81  
 3rd Qu.:51.00   3rd Qu.:35.50   3rd Qu.:4.000   3rd Qu.:40.00  
 Max.   :55.00   Max.   :39.00   Max.   :9.000   Max.   :42.00

Redefining three.plots()

three.plots <- function(input) {
  plot(sex ~ weight, data=input)
  plot(weight ~ sex, data=input, boxwex=0.2, notch=TRUE, col="grey")
  plot(sex ~ apgar5, data=input)
}

New function

par(mfrow=c(1,3))
three.plots(healthy)

But now…

three.plots()
Error in eval(m$data, eframe): argument "input" is missing, with no default

It doesn’t work as before

Redefining three.plots() again

three.plots <- function(input=birth) {
  plot(sex ~ weight, data=input)
  plot(weight ~ sex, data=input, boxwex=0.2, notch=TRUE, col="grey")
  plot(sex ~ apgar5, data=input)
}

And now…

par(mfrow=c(1,3))
three.plots()

Thanks for your attention