plotrange.bygene(ProGenExpress)R Documentation

Plot numerical values on a genome setting the range by gene name

Description

Draws a plot showing numerical values on the genome of prokaryotes, using gene names to identify the region to plot

Usage

plotrange.bygene(linked = NULL, cnames = "M", start = NULL, stop = NULL, pad = 0,
                 match.gname = "Gene", display.gname = "Gene", vertical = FALSE, ...)

Arguments

linked A data frame consisting of gene names, locations on the genome and numerical values to be plotted. Must have numerical columns "Start" and "Stop" indicating the location on the genome of genes or features
cnames Vector of column names in linked which contain the numerical values to be plotted
start The gene name for the first gene to be plotted
stop The gene name for the last gene name to be plotted
pad A numerical value - number of bases beyond start and stop to encompass
match.gname The column name in linked to which start and stop refer (e.g. "Gene" or "Synonym")
display.gname The column name in linked which contains the text to be printed on the genome plot (e.g. "Gene" or "Synonym")
vertical Whether the genome should be plotted vertically or not
... Other arguments, e.g. for controlling highlight areas, will be passed to plotrange or plotrange.vertical

Details

Internally the function used PGE.barplot. It calls either plotrange or plotrange.vertical depending on the value of the vertical argument

Value

A graph is plotted on the current device

Author(s)

Michael Watson

See Also

plotrange.vertical, plotrange

Examples


        # load the IFR microarray data
        data(IFR)

        # read in an NCBI .ptt file for S typhimurium
        data(STLT2) # produced by 'STLT2 <- read.ptt("NC_003197.ptt")'

        # link the genome and the microarray data
        # we want one value per gene and so we average over the values
        linked <- linkem.avg(STLT2,IFR,"Synonym","Synonym",cnames=c("M4h","M8h","M12h"))

        # create an image of Spi-1
        x11()
        highlight <- data.frame(start="sitA", stop="invH", name="spi-2", color="yellow")
        plotrange.bygene(linked, start="sitA", stop="invH", cnames=c("M4h","M8h","M12h"),
                                pad=5000, highlight=highlight)

        # plot the same but taking into account intergenic distance
        x11()
        plotrange.bygene(linked, start="sitA", stop="invH", cnames=c("M4h","M8h","M12h"),
                                pad=5000, highlight=highlight, distscale=100)
[Package ProGenExpress version 1.0 Index]