plotKegg {FGNet} | R Documentation

## Plot KEGG pathway

### Description

DEPRECATED. KEGGprofile seems to be no longer mantained. You may use this function by manually downloading the pathway XML.

Plots KEGG pathway with the given genes.

### Usage

    plotKegg(keggIDs, geneExpr, geneIDtype = "ENSEMBL",
        colType = c("continuous", "discrete"))

### Arguments

`keggIDs` | character vector. KEGG IDS with prefix.
`geneExpr` | named numeric vector. Names should contain the gene ID, the value the gene expression. NA is accepted as expression value.
`geneIDtype` | character vector. Type of gene identifier.
`colType` | "continuous" or "discrete" determines the color of the genes.

### Details

Color code:

- Green: Negative expression.

- Red: Positive expression.

- Light yellow: Expression zero or very close to zero.

- Blue: Expression not available.

- White: Gene not in list.

### Value

The pathway plot is saved in the current working directory.

### See Also

Overview of the package: `FGNet`

Package tutorial: `vignette("FGNet-vignette")`

### Examples

    ###################################
    # Gene info
    genesYeast <- c("ADA2", "APC1", "APC11", "APC2", "APC4", "APC5", "APC9", "CDC16",
        "CDC23", "CDC26", "CDC27", "CFT1", "CFT2", "DCP1", "DOC1", "FIP1",
        "GCN5", "GLC7", "HFI1", "KEM1", "LSM1", "LSM2", "LSM3", "LSM4",
        "LSM5", "LSM6", "LSM7", "LSM8", "MPE1", "NGG1", "PAP1", "PAT1",
        "PFS2", "PTA1", "PTI1", "REF2", "RNA14", "RPN1", "RPN10", "RPN11",
        "RPN13", "RPN2", "RPN3", "RPN5", "RPN6", "RPN8", "RPT1", "RPT3",
        "RPT6", "SGF11", "SGF29", "SGF73", "SPT20", "SPT3", "SPT7", "SPT8",
        "TRA1", "YSH1", "YTH1")

    # Gene expression (1=UP, -1=DW)
    genesYeastExpr <- setNames(c(rep(1,29), rep(-1,30)), genesYeast)

    ###################################
    # Plot pathway

    # Specific pathway
    # plotKegg("sce04111", genesYeastExpr, geneIDtype="GENENAME")

    # Pathways from analysis:
    txtFile <- paste(file.path(system.file('examples', package='FGNet')),
        "DAVID_Yeast_raw.txt", sep="/")
    results <- format_david(txtFile, jobName="DavidAnalysis")

    keggTerms <- unlist(getTerms(results, returnValue="KEGG"))

    # plotKegg(keggTerms, ... geneIDtype="ENSEMBL")

[Package FGNet version 3.16.0 Index]