plotKegg: Plot KEGG pathway

Description Usage Arguments Details Value See Also Examples

Description

Plots KEGG pathway with the given genes.

Usage

1
2
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
###################################
# 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")


Search within the FGNet package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.