Dr. Mark Gardener

 
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Statistics for Ecologists Edition 2 COver

Statistics for Ecologists Using R and Excel.

Edition 2.

Statistics for Ecologists Using R and Excel:
Data collection, exploration, analysis and presentation

Pelagic Publishing

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Writer's Bloc

On this page you can find out about my latest writing project. I'll post updates on progress, tables of contents and also some of the R scripts (and possibly Excel spreadsheets) I am developing in support of the new book. I'll try to keep the material reasonably up to date.

The Writer's Bloc homepage contains a table of contents and an index of the pages that contain custom R commands and R scripts.


I am working on a new edition of my book Statistics for Ecologists Using R and Excel. I am currently revising the chapter(s) on graphics and thought I'd make some notes about gridlines on graphs...


Gridlines on Excel charts and R plots:

Introduction

Gridlines are potentially useful items you might want to incorporate in your charts. Gridlines can help the reader to gauge the height of bars in a column chart more easily for example, and so the readability is improved.

On the other hand gridlines can "get in the way" and hinder readability by making your chart cluttered. In scatter plots you may require both horizontal and vertical gridlines, having gridlines on one axis only can "lead the eye". Knowing when to apply gridlines or not is part of the skill of presentation.

Gridlines are added and edited easily in Excel. In R you can add gridlines using the abline() command.


In Excel the Chart Tools menus allow you to add or edit gridlines.

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Gridlines in Excel charts

You can easily add gridlines using Excel. Many chart templates incorporate them (sometimes when you do not require) and once you have a chart you can easily add them via the Chart Tools menus. In Excel 2013 there is an Add Chart Element button (you can also use the + button that appears beside a chart you have clicked on).


In Excel 2013 you can use the Add Chart Element button to add gridlines.

In previous versions of Excel (e.g. 2010) you can find the Gridlines button on the Layout menu of the Chart Tools.

Adding gridlines in Excel 2010
In Excel 2010 the Gridlines button is in the Layout menu of the Chart Tools.

In R you can add gridlines using the abline() command. You use abline(h = x, ...) for horizontal lines or abline(v= x, ...) for vertical lines. You specify x, the value(s) where you want the lines to appear. The ... means that you can specify additional graphical parameters to format the gridlines; such as colour, line style and so on.


Edit gridlines in Excel using the Chart Tools menu.

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Editing Excel gridlines

Once you have added your Excel gridlines you can choose to alter their appearance. You can double-click or right-click on the gridlines directly or you can use the Current Selection section of the Chart Tools > Format menu, which allows you to select, then format chart elements.

Selectiion menu section of the Chart Tools
The Selection section of the Chart Tools makes it easy to
select and format chart elements, including gridlines.

Once you have chosen to format the gridlines you will be presented with a range of formatting options, allowing you to choose the colour, width and style for example. You may not want the gridlines to be too bold so a mid-gray and dashed line might be more appropriate than a solid black line.


Alter the format of Excel column chart bars to semi-transparent to allow gridlines to be visible through the bars.

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Altering Excel gridline visibility

By default your chart colours will be solid. This means that on a column chart the gridlines will disappear behind the bars and only be visible between them.

In most cases this is exactly what you want but there may be occasions when you want to see the gridlines through the bars. You can edit the data series and choose to alter the transparency of the bars (on a column chart).

The format gridlines dialogue box
Altering transparency of column chart bars allows the gridlines to be visible through the bars.

You can easily change the level of transparency to get the effect you want.

Excel bar chart with semi-transparent bars allows the gridlines to be visible
An Excel column chart with semi-transparent bars
allows the gridlines to be visible through the bars.

Of course generally you won't want to allow the gridlines to be visible through the bars but it is a handy trick to have up your sleeve.


Use abline() to add gridlines on R plots

Use abline(h = x, ...) for horizontal lines.

Use abline(v = x, ...) for vertical lines.

Additional graphical parameters can alter the line appearance.

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Gridlines in R plots

Use the abline() command to add gridlines to R plots. The command adds straight lines to existing plots. You can use the command to add a line of best-fit by specifying intercept and slope (indeed the command can read the results of other commands that produce coefficients), but for gridlines you can use one of the following:

  • abline(h = x, ...) For horizontal lines.
  • abline(v = x, ...) For vertical lines.

You specify x, which is the position of the line(s). You can use various methods to produce a set of values that define the position of the lines:

Command Detail
c(...) Give the values explicitly, separated by commas.
start:end Give the start and end points, this will produce a primitive sequence with an interval of 1.
seq(from = , to = , by = ) Make a sequence, you specify start and end points and the interval.
pretty(start:end, n) Makes a sequence from a simple range (start:end) that is split into "pretty" intervals. You also give n, which is an idealized number of intervals. The command does its best to produce n items.

The seq() command is probably the easiest to use as the results are completely defined by the user. The pretty() command is generally used internally to make the plot axes intervals so using it would likely match the axis. However, you may not want gridlines at exactly the same intervals so it's probably best to stick to seq().

You can use various additional parameters to alter the appearance of the lines for example:

Parameter Detail
col The colour of the line(s). Usually as a "name" but you can specify an integer, which will use a colour from the current colour palette.
lwd The width of the line. Think of it as an expansion factor. Values >1 make the line wider, whilst values <1 make it thinner.
lty The line type, 0 = none, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash. You can also specify the type as a "string" that matches the names given here.

The abline() command thus gives you good control over the position and format of gridlines.


To hide gridlines behind plot elements re-plot using
add = TRUE for a barplot() or boxplot().

For a scatter plot use
plot(x, y, type = "n")
then add the data using the points() command after drawing gridlines.

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Place gridlines behind other R plot elements

When you add gridlines to an R plot your lines will usually over-top any points or bars that were present.

Gridlines in an R plot over-top the bars
Gridlines added to an existing plot will overlay the existing chart elements.

It may be that this is what you want, but generally it is desirable to have the gridlines disappear behind the bars. If you are drawing gridlines to a barplot() or a boxplot() then you can easily achieve this by re-plotting and adding add = TRUE in the plotting command.

Gridlines drawn behind existing plot elements
Use add = TRUE to redraw bars and so overtop any gridlines.

If you are using a scatter plot and the regular plot() command you take a different approach.

    1. Use the plot() command but set type = "n" to create the plot but not any points.
    2. Add the gridlines using abline() commands.
    3. Add the data points using the points() command.

These simple "tricks" should ensure that your gridlines end up where you want them.


Example of drawing a bar chart with gridlines behind the bars.

Error bars added afterwards using arrows() command.

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Example code

The bar chart with error bars shown earlier was drawn using the following code:

> hog3 # The data
  Upper Mid Lower
1     3   4    11
2     4   3    12
3     5   7     9
4     9   9    10
5     8  11    11
6    10  NA    NA
7     9  NA    NA

# Get median values for each column

> med = apply(hog3, MARGIN = 2, median, na.rm = TRUE)

# Get the upper and lower quartiles, which will form the error bars

> up = apply(hog3, MARGIN = 2, quantile, na.rm = TRUE, prob = 0.75)

> dn = apply(hog3, MARGIN = 2, quantile, na.rm = TRUE, prob = 0.25)

> dat <- rbind(med, up, dn) # Make a matrix of the data and error bars
> dat
    Upper Mid Lower
med   8.0   7    11
up    9.0   9    11
dn    4.5   4    10

# Draw the bar chart

> barplot(dat["med",], col = "lightblue")

# Add the gridlines

> abline(h = seq(2,10,2), lty = "dashed", col = "gray30")

# Add axis titles

> title(xlab = "Sample Site", ylab = "Abundance")

# Re-draw plot and add to existing. Note the plot is given a name, which allows the x-values for the error bars to be calculated.

> bp <- barplot(dat["med",], col = "lightblue", add = TRUE)

# Draw the error bars using the inter-quartile values

> arrows(bp,dat["up",], bp,dat["dn",], length = 0.1, angle = 90, code = 3)


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Providing training for:

  • Ecology
  • Data analysis
  • Statistics
  • R The statistical programming language
  • Data management
  • Data mining

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