canprot (version 1.0.0)

rankplot: Plot Ranking of Chemical Affinities

Description

Plot ranking of chemical affinities of groups of proteins.

Usage

rankplot(pdat, T = 37, what = "rankdiff", main = NULL, res = 300,
           plot.it = TRUE, xlim = c(-75, -55), ylim = c(-10, 10))

Arguments

pdat

list, data object generated by a pdat_ function

T

numeric, temperature in degrees Celsius

what

character, “rankdiff” or “affinity”

main

character, text to use for title of plot

res

numeric, grid resolution for plot

plot.it

logical, draw a plot?

xlim

numeric, range of x-axis ()

ylim

numeric, range of y-axis ()

Details

This function creates a - diagram showing the relative stabilities of the two groups of proteins in the specified dataset. These groups consist of the relatively down- and up-expressed proteins identified by up2 in one of the pdat_ functions.

The function generates a colored image and contour plot showing the weighted difference of sums of ranks of chemical affinities of formation of proteins in the two groups (see affinity and rankdiff). Increasing intensity of blue or red colors (see get_colors) represent higher rankings of the down-expressed (up2==FALSE) or up-expressed (up2==TRUE) proteins, respectively. Alternatively, if what is “affinity”, a maximum affinity diagram is produced (see diagram in CHNOSZ), with fields colored red or blue according to the relative expression of the protein.

If main is NULL, the title for the plot is taken from the description supplied in pdat.

Set plot.it to FALSE to skip the plotting and instead return a list containing the computed rank differences and x- and y- values and labels.

See Also

This function is used in groupplots.

Examples

# NOT RUN {
library(CHNOSZ)
pdat <- pdat_colorectal("JKMF10")
rankplot(pdat, res=25)
rankplot(pdat, res=25, what="affinity")
# }