# plotMAhex

##### MA-plot using hexagon bins

Creates an MA-plot using hexagons with color/glyph coding for control spots.

- Keywords
- hplot

##### Usage

```
plotMAhex(MA, array = 1, xlab = "A", ylab = "M",
main = colnames(MA)[array], xlim = NULL, ylim = NULL,
status = NULL, values, pch, col, cex, nbin = 40,
zero.weights = FALSE, style = "colorscale", legend = 1.2,
lcex = 1, minarea = 0.04, maxarea = 0.8, mincnt = 2,
maxcnt = NULL, trans = NULL, inv = NULL, colorcut = NULL,
border = NULL, density = NULL, pen = NULL,
colramp = function(n) { LinGray(n, beg = 90, end = 15) },
newpage = TRUE, type = c("p", "l", "n"),
xaxt = c("s", "n"), yaxt = c("s", "n"),
verbose = getOption("verbose"))
```

##### Arguments

- MA
an

`RGList`

,`MAList`

or`MArrayLM`

object, or any list with components`M`

containing log-ratios and`A`

containing average intensities. Alternatively a`matrix`

,`Affybatch`

or`ExpressionSet`

object.- array
integer giving the array to be plotted. Corresponds to columns of

`M`

and`A`

.- xlab, ylab, main
character strings giving label for x-axis, y-axis or main tile of the plot.

- xlim, ylim
numeric vectors of length 2 giving limits for x-axis (or y-axis respectively), defaulting to min and max of the data.

- status
character vector giving the control status of each spot on the array, of same length as the number of rows of

`MA$M`

. If omitted, all points are plotted in the default color, symbol and size.- values
character vector giving values of

`status`

to be highlighted on the plot. Defaults to unique values of`status`

. Ignored if there is no`status`

vector.- pch
vector or list of plotting characters. Default to integer code 16. Ignored is there is no

`status`

vector.- col
numeric or character vector of colors, of the same length as

`values`

. Defaults to`1:length(values)`

. Ignored if there is no`status`

vector.- cex
numeric vector of plot symbol expansions, of the the same length as

`values`

. Defaults to 0.2 for the most common status value and 1 for the others. Ignored if there is no`status`

vector.- nbin
Number of bins

- zero.weights
logical, should spots with zero or negative weights be plotted?

- style
string specifying the style of hexagon plot, see

`grid.hexagons`

for the possibilities.- legend
numeric width of the legend in inches of

`FALSE`

. In the latter case, or when`0`

, no legend is not produced.- lcex
characters expansion size for the text in the legend.

- minarea
fraction of cell area for the lowest count.

- maxarea
fraction of the cell area for the largest count.

- mincnt
cells with fewer counts are ignored.

- maxcnt
cells with more counts are ignored.

- trans
`function`

specifying a transformation for the counts such as`sqrt`

.- inv
the inverse transformation of

`trans`

.- colorcut
vector of values covering [0, 1] that determine hexagon color class boundaries and hexagon legend size boundaries. Alternatively, an integer (

`<= maxcnt`

) specifying the*number*of equispaced colorcut values in [0,1].- border, density, pen
color for polygon borders and filling of each hexagon drawn, passed to

`grid.hexagons`

.- colramp
function accepting an integer

`n`

as an argument and returning n colors.- newpage
should a new page start?

- type, xaxt, yaxt
strings to be used (when set to

`"n"`

) for suppressing the plotting of hexagon symbols, or the x- or y-axis, respectively.- verbose
logical indicating if some diagnostic output should happen.

##### Details

An MA-plot is a plot of log-intensity ratios (M-values) versus
log-intensity averages (A-values). If `MA`

is an `RGList`

or
`MAList`

then this function produces an ordinary within-array
MA-plot. If `MA`

is an `MArrayLM`

object, then the plot is an
fitted model MA-plot in which the estimated coefficient is on the y-axis
and the average A-value is on the x-axis.

If `MA`

is a `matrix`

or `ExpressionSet`

object, then this
function produces a between-array MA-plot. In this case the A-values in
the plot are the average log-intensities across the arrays and the
M-values are the deviations of the log-intensities for the specified
array from the average. If there are more than five arrays, then the
average is computed robustly using medians. With five or fewer arrays,
it is computed by means.

The `status`

vector is intended to specify the control status of
each spot, for example "gene", "ratio control", "house keeping gene",
"buffer" and so on. The vector is usually computed using the function
`controlStatus`

from package limma and a
spot-types file. However the function may be used to highlight any
subset of spots.

The arguments `values`

, `pch`

, `col`

and `cex`

can be included as attributes to `status`

instead of being
passed as arguments to `plotMA`

.

See `points`

for possible values for `pch`

,
`col`

and `cex`

.

##### Value

A plot is created on the current graphics device. and a list with the following items is returned invisibly:

the `hexViewport`

constructed and used.

if a legend has been produced, its
`viewport`

.

a `hexbin`

object built with A as the x coordinate
and M as the y coordinate.

##### References

##### See Also

`plotMA`

from package limma,
and `gplot.hexbin`

.

##### Examples

`library(hexbin)`

```
# NOT RUN {
if(require(marray)){
# }
# NOT RUN {
<!-- %% for the data only --> data(swirl, package="marray") -->
# }
# NOT RUN {
data(swirl)
hb <- plotMAhex(swirl[,1],newpage=FALSE,
main = "M vs A plot with hexagons", legend=0)
hexVP.abline(hb$plot.vp,h=0,col=gray(.6))
hexMA.loess(hb)
}
# }
```

*Documentation reproduced from package hexbin, version 1.27.1, License: GPL-2*