singleDomainPlotting {PhyloProfile} | R Documentation |
Create architecure plot for a single protein
singleDomainPlotting(df, geneID = "GeneID", sep = "|", labelSize = 12, titleSize = 12, minStart = NULL, maxEnd = NULL, colorScheme)
df |
domain dataframe for ploting containing the seed ID, ortholog ID, ortholog sequence length, feature names, start and end positions, feature weights (optional) and the status to determine if that feature is important for comparison the architecture between 2 proteins* (e.g. seed protein vs ortholog) (optional). |
geneID |
ID of seed or orthologous protein |
sep |
separate indicator for title. Default = "|". |
labelSize |
lable size. Default = 12. |
titleSize |
title size. Default = 12. |
minStart |
the smallest start position of all domains |
maxEnd |
the highest stop position of all domains |
colorScheme |
color scheme for all domain types |
Domain plot of a single protein as a ggplot object.
Vinh Tran tran@bio.uni-frankfurt.de
getQualColForVector
,
parseDomainInput
## Not run: # get domain data domainFile <- system.file( "extdata", "domainFiles/101621at6656.domains", package = "PhyloProfile", mustWork = TRUE ) domainDf <- parseDomainInput(seedID, domainFile, "file") df <- domainDf[ domainDf$orthoID == "101621at6656|AGRPL@224129@0|224129_0:001955|1",] # create color scheme for all domain types allFeatures <- levels(as.factor(df$feature)) allColors <- getQualColForVector(allFeatures) colorScheme <- structure( allColors, .Names = allFeatures ) # other parameters geneID <- "AGRPL@224129@0|224129_0:001955|1" sep <- "|" labelSize <- 9 titleSize <- 9 minStart <- min(df$start) maxEnd <- max(df$end) # do plotting singleDomainPlotting( df, geneID, sep, labelSize, titleSize, minStart, maxEnd, colorScheme ) ## End(Not run)