plotKegg: Plot KEGG pathway

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:

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")

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

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