sherlock85 - 2 months ago 20

R Question

How can I generate the following plot in R? Points, shown in the plot are the averages, and their ranges correspond to minimal and maximal values.

I have data in two files (below is an example).

`x y`

1 0.8773

1 0.8722

1 0.8816

1 0.8834

1 0.8759

1 0.8890

1 0.8727

2 0.9047

2 0.9062

2 0.8998

2 0.9044

2 0.8960

.. ...

Answer

First of all: it is very unfortunate and surprising that **R cannot draw error bars "out of the box"**.

Here is my favourite workaround, the advantage is that you *do not need any extra packages*. The trick is to draw arrows (!) but with little horizontal bars instead of arrowheads (!!!). This not-so-straightforward idea comes from the R Wiki Tips and is reproduced here as a worked-out example.

Let's assume you have a vector of "average values" `avg`

and another vector of "standard deviations" `sdev`

, they are of the same length `n`

. Let's make the abscissa just the number of these "measurements", so `x <- 1:n`

. Using these, here come the plotting commands:

```
plot(x, avg,
ylim=range(c(avg-sdev, avg+sdev)),
pch=19, xlab="Measurements", ylab="Mean +/- SD",
main="Scatter plot with std.dev error bars"
)
# hack: we draw arrows but with very special "arrowheads"
arrows(x, avg-sdev, x, avg+sdev, length=0.05, angle=90, code=3)
```

The result looks like this:

In the `arrows(...)`

function `length=0.05`

is the size of the "arrowhead" in inches, `angle=90`

specifies that the "arrowhead" is perpendicular to the shaft of the arrow, and the particularly intuitive `code=3`

parameter specifies that we want to draw an arrowhead on both ends of the arrow.

For horizontal error bars the following changes are necessary, assuming that the `sdev`

vector now contains the errors in the `x`

values and the `y`

values are the ordinates:

```
plot(x, y,
xlim=range(c(x-sdev, x+sdev)),
pch=19,...)
# horizontal error bars
arrows(x-sdev, y, x+sdev, y, length=0.05, angle=90, code=3)
```