Up: Component summary
Up: Component summary
Component
MDSPlot
Plots multidimensional scaling of numeric data. An optional
SampleGroupTable can be given to color groups differently
in the plot or to use only a subset of columns from the input
data.
| Version | 2.2 |
|---|---|
| Bundle | tools |
| Categories | Quality Control Latex |
| Authors | Kari Nousiainen (Kari.Nousiainen@Helsinki.FI), Viljami Aittomaki (viljami.aittomaki@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R ; scatterplot3d (R-package) ; cluster (R-package) |
| Source files | component.xml MDSPlot.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| expr | Matrix | Mandatory | Numeric data matrix |
| groups | SampleGroupTable | Optional | Optional table that maps expr columns (i.e.
samples) to groups. Only samples in valid groups are used for
computing and plotting MDS. Groups are indicated with color. A
sample may be included in several groups, but is used only once
for computing MDS. Groups of type ratio are
ignored. |
Outputs| Name | Type | Description |
|---|---|---|
| mdsCoOrdinates | Matrix | The co-ordinates of the samples after multidimensional scaling. |
| report | Latex | A LaTeX document containing a scatter plot of the scaled samples (if plotting is possible). |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| caption | string | "Multidimensional Scaling" | Caption for the LaTeX figure. |
| cex | float | 1.0 | Scaling factor for point symbols or sample names in plot. |
| colorFunction | string | "" | Custom function for colors. For example c('red', 'blue',
'green'), rainbow(3) or
rainbow(%d), in which %d is replaced
with the number of groups plotted. Default colors start from
black and continue with colors from the rainbow
function. |
| dimensions | int | 2 | Number of dimensions the data is scaled into. |
| pagebreak | boolean | false | If true, the output LaTeX report starts with a page break. |
| pch | int | 1 | Defines point symbol for plotting. See help for
points function in R. Ignored if
plotNames is true. |
| plotLegend | boolean | true | If true, a group legend is plotted, else no legend is shown.
Ignored if groups is not present. |
| plotNames | boolean | true | If true, sample names are plotted in the scatter plot,
else symbols defined by pch are used. |
| sectionTitle | string | "Multidimensional Scaling" | Title of the LaTeX section. If empty, no section statement is written. |
| sectionType | string | "subsection" | Type of LaTeX section. One of section, subsection or subsubsection. If empty, no section statement is written. |
| width | float | 16 | Width of plot figure in cm. |
Test cases| Test case | Parameters▼ | IN expr |
IN groups |
OUT mdsCoOrdinates |
OUT report |
|
|---|---|---|---|---|---|---|
| case1 | (missing) | expr | (missing) | mdsCoOrdinates | report | |
| case2-groups | properties | expr | groups | mdsCoOrdinates | report | |
|
caption=Ducks sporting, |
||||||
| case3-similarSamples | properties | expr | (missing) | mdsCoOrdinates | report | |
|
dimensions=3, |
||||||
| case4-failIdenticalSamples | (missing) | expr | (missing) | (expecting failure) | (expecting failure) | |
| case5-failTooFewSamples | properties | expr | groups | (expecting failure) | (expecting failure) | |
|
dimensions=2 |
||||||