plotPmat {aSPU} | R Documentation |

## Image plot of P-value matrix.

### Description

It gives a P-value image for a given P-value matrix.

### Usage

```
plotPmat(
Ps,
zlim = NULL,
main = NULL,
yt = NULL,
xlab = "SNPs",
thresh = -log(5e-08, 10),
trait.names = NULL
)
```

### Arguments

`Ps` |
P-value matrix. Row represent traits, column represent SNPs |

`zlim` |
-log 10 transformed p value range. |

`main` |
main title. |

`yt` |
it controls the location of trait names. |

`xlab` |
lable for x axis. Default is "SNPs". |

`thresh` |
Default is set to widely used genome wise threshold -log(5e-8,10). |

`trait.names` |
A vector of trait names. |

### Value

Image of P-values matrix.

### Author(s)

Il-Youp Kwak and Wei Pan

### References

Il-Youp Kwak, Wei Pan (2017) Gene- and pathway-based association tests for multiple traits with GWAS summary statistics, Bioinformatics. 33(1), 64-71

### See Also

### Examples

```
## Say we have 3 traits and their p-values at 5 SNPs.
Ps <- rbind( c(0.001, 0.4, 0.5, 0.00000001, .1),
c(0.03, 0.3, 0.3, 0.00001, .2),
c(0.01, 0.2, 0.4, 0.001, .0001) )
## We can visualize it using plotPmat function.
plotPmat(Ps)
```

[Package

*aSPU*version 1.50 Index]