plot.GGInetwork {GeneGeneInteR} | R Documentation

## Plot a Gene-Gene Interaction Study with an heatmap-like visualization

### Description

`GGI.plot` is a graphical function that allow a heatmap-like or a network-like visualization of a Gene-Gene Interaction study based on a set of genes.

### Usage

    ## S3 method for class 'GGInetwork'
    plot(x,method=c("heatmap","network"),threshold=NULL,
    col=c("#D6604D","#104E8B"),colbar.width=0.15, title=NULL,hclust.order=FALSE,
    use.log=FALSE,NA.col="#D3D3D3",draw.pvals=NULL,
    draw.names=NULL,interact=FALSE,
    method.adjust=c("none","holm","hochberg","hommel","bonferroni","BH","BY","fdr"),
    genes=seq_len(ncol(x$p.value)), plot.nointer=TRUE, ...)

### Arguments

`x` | `GGInetwork`. Given as output of `GGI`.
`method` | Output graph ("heatmap" for heatmap-like, "network" for network-like). Default is `heatmap`.
`threshold` | A numeric between 0 and 1. All p-value strictly greater than that `threshold` are distinctly colored (See `NA.col`). Default is `NULL` corresponding to no threshold for applied for an heatmap graph and a 0.05 threshold applied for the network representation.
`method.adjust` | correction method for multiple testing as proposed in the `p.adjust` function. By default, no correction is applied to the p-values.
`genes` | Numeric vector allowing a selection of the genes that will be included in the relations. Default is set to all genes.
`col` | (Only for `method=heatmap`.) String vector. Marker colors to be used for the gradient. The first element of the vector is the value for 0 and the last is for 1. If only one value is parsed, that color is used for 0 and white is automatically used for 1. Any value compatible with `colorRampPalette` function.
`colbar.width` | (Only for `method=heatmap`.) A positive number describing the gradient bar width ratio. That number is used to keep the gradient bar's width steady as the size of `GGI` increases.
`title` | (Only for `method=heatmap`.) A string used as the plot title. If left as NULL, a generic name is generated.
`hclust.order` | (Only for `method=heatmap`.) A boolean. Should a hierachical clustering procedure be performed on `GGI` to order the matrix ?
`use.log` | (Only for `method=heatmap`.) A boolean. Should the p-values be reported in -log10? FALSE by default.
`NA.col` | (Only for `method=heatmap`.) A string. The color used when a p-value is strictly greater than `threshold`.
`draw.pvals` | (Only for `method=heatmap`.) Either NULL or a boolean. Should p-values be plotted ? Disabled when the size of `GGI` exceeds 15*15.
`draw.names` | (Only for `method=heatmap`.) Either NULL or a boolean. Should genes' names be plotted on matrix margins? Disabled when the size of `GGI` exceeds 25*25.
`interact` | (Only for `method=heatmap`.) A boolean. Should the plot be clickable ? (See Details for more information). Disabled when open R session is not interactive.
`plot.nointer` | (Only for `method=network`.) A boolean. Set TRUE if the genes with no interaction should be plotted.
`...` | further arguments passed to or from other methods.

### Details

If `method=heatmap`, this function draw the upper half of a Gene-Gene Interaction results matrix without its diagonal. A gradient is created from 0 to 1 (by default from crimson to white) and the matrix cells are colored according to the corresponding p-value.

By default, when `draw.pvals==NULL` and `draw.names==NULL`, p-values and names are drawn to make matrix reading easier, but in case parameter `GGI` is large, p-values (and eventually gene names as `GGI` grows bigger) are not drawn. In that case, the default behavior of the function is to start an interactive process where user can click on a cell of interest to open a tooltip displaying which genes are involved in selected interaction and the p-value of the interaction test. Tooltips can be closed if user clicks anywhere else than on a cell. This process stops when the user presses the escape button (or terminates the locator procedure in general) or when the user clicks on any place other than a cell when no tooltip window is open.

To improve plot clarity, user may set a threshold above which cells are colored with a distinct color. By default, threshold is set to 1 and no cell is colored differently (as values must be strictly above the threshold).

If `method=network`, this function plots a graph representing the significative interactions between genes of a Gene-Gene Interaction study.

### Value

The form of the value returned by `plot` depends on the class of its argument. See Details.

### See Also

`GGI`

### Examples

    ## Not run:
    ## Dataset is included in the package
    ped <- system.file("extdata/example.ped", package="GeneGeneInteR")
    info <- system.file("extdata/example.info", package="GeneGeneInteR")
    posi <- system.file("extdata/example.txt", package="GeneGeneInteR")

    ## Importation of the genotypes
    data.imported <- importFile(file=ped, snps=info, pos=posi, pos.sep="\t")
    ## Filtering of the data: SNPs with MAF < 0.05 or p.value for HWE < 1e-3 or
    ## call rate < 0.9 are removed.
    data.scour <- snpMatrixScour(snpX=data.imported$snpX,genes.info=data.imported$genes.info,
                                  min.maf=0.05,min.eq=1e-3,call.rate=0.9)
    ## Imputation of the missing genotypes
    data.imputed <- imputeSnpMatrix(data.scour$snpX, genes.info = data.scour$genes.info)

    ## Importation of the phenotype
    resp <- system.file("extdata/response.txt", package="GeneGeneInteR")
    Y  <- read.csv(resp, header=FALSE)

    ## plot of the interaction between the 17 genes with the CLD method -- can take a few minutes
    GGI.res <- GGI(Y=Y, snpX=dta$snpX, genes.info=dta$genes.info,method="CLD")
    plot(GGI.res,threshold=0.05)

    ## Selection of 12 genes among 17
    data.select <- selectSnps(data.imputed$snpX, data.imputed$genes.info, c("bub3","CDSN","Gc","GLRX",
                              "PADI1","PADI2","PADI4","PADI6","PRKD3","PSORS1C1","SERPINA1","SORBS1"))
    GGI.res <- GGI(Y=Y, snpX=data.select$snpX, genes.info=data.select$genes.info,method="PCA")

    ## End(Not run)
    ## Equivalent importation of the GGI.res object
    load(system.file("extdata/GGIRes.Rdata", package="GeneGeneInteR"))

    ## Plot of the results with default values
    plot(GGI.res)

    ## Plot of the results with a threshold and an ordering of the genes.
    ## Default method is an heatmap-like representation
    plot(GGI.res,threshold=0.1,hclust.order=TRUE)

    ## Example of network with default threshold 0.05
    plot(GGI.res,method="network")

    ## Example of network with threshold 0.01 where genes with no interaction are not plotted
    # (plot.nointer=FALSE)
    plot(GGI.res,method="network",threshold=0.1,plot.nointer=FALSE)

[Package GeneGeneInteR version 1.12.0 Index]