# inGraphs

##### inGraphs: InPosition plotting function

InPosition plotting function which is an interface to `prettyGraphs`

.

- Keywords
- multivariate, misc, bootstrap, permutation, graphs

##### Usage

```
inGraphs(res, DESIGN = NULL, x_axis = NULL, y_axis = NULL, inference.info = NULL,
color.by.boots = TRUE, boot.cols = c("plum4", "darkseagreen", "firebrick3"),
fi.col = NULL, fi.pch = NULL, fj.col = NULL, fj.pch = NULL, col.offset = NULL,
constraints = NULL, xlab = NULL, ylab = NULL, main = NULL, bootstrapBars = TRUE,
correlationPlotter = TRUE, biplots = FALSE)
```

##### Arguments

- res
results from InPosition or ExPosition. If results are from ExPosition,

`inference.info`

must be included.- DESIGN
A design matrix to apply colors (by pallete selection) to row items

- x_axis
which component should be on the x axis?

- y_axis
which component should be on the y axis?

- inference.info
Inference data as output by InPosition (of class inpoOutput).

- color.by.boots
a boolean. If TRUE, items are colored by bootstrap ratio test. Items larger than

`critical.value`

are colored 'plum4' on the horizontal component, 'darkseagreen' on the vertical component, or 'firebrick3' if the item is significant on both components (to be visualized). If FALSE, the color of the items will be used.- boot.cols
vector of colors:

`c(horizontal component color, vertical component color, color when item is significant on both)`

.- fi.col
A matrix of colors for the row items. If NULL, colors will be selected.

- fi.pch
A matrix of pch values for the row items. If NULL, pch values are all 21.

- fj.col
A matrix of colors for the column items. If NULL, colors will be selected.

- fj.pch
A matrix of pch values for the column items. If NULL, pch values are all 21.

- col.offset
A numeric offset value. Is passed to

`createColorVectorsByDesign`

.- constraints
Plot constraints as returned from

`prettyPlot`

. If NULL, constraints are selected.- xlab
x axis label

- ylab
y axis label

- main
main label for the graph window

- bootstrapBars
a boolean. If TRUE (default), bootstrap ratio bar plots will be created.

- correlationPlotter
a boolean. If TRUE (default), a correlation circle plot will be created. Applies to PCA family of methods (CA is excluded for now).

- biplots
a boolean. If FALSE (default), separate plots are made for row items ($fi) and column items ($fj). If TRUE, row ($fi) and column ($fj) items will be on the same plot.

##### Value

Currently, nothing is returned. This function, for now, works as a visualizer for inference tests. Colors and constraints come from the descriptive (fixed effects) analysis.

##### See Also

##### Examples

```
# NOT RUN {
data(ep.iris)
data<-ep.iris$data
design<-ep.iris$design
gpca.iris.res <- epGPCA.inference.battery(data,DESIGN=design,make_design_nominal=FALSE)
inGraphs(gpca.iris.res,y_axis=3)
# }
```

*Documentation reproduced from package InPosition, version 0.12.7.1, License: GPL-2*