Autoplotprotein (version 1.1)

plotsite: ploting site

Description

Draw the protein site

Usage

plotsite()

Value

Location of the site in the protein

Details

The tool ennable visualization of amino acid changes at the protein level,The scale of a protein domain and the position of a functional motif/site will be precisely defined. The features available include site

References

https://cran.r-project.org/doc/manuals/R-exts.html

See Also

codehelp

Examples

# NOT RUN {
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function () 
{
    protein = read.table("Protein.txt", sep = "\t", stringsAsFactors = F)
    domain = read.table("Domain.txt", sep = "\t", stringsAsFactors = F)
    length = read.table("Length.txt", sep = "\t", stringsAsFactors = F)
    site = read.table("Site.txt", sep = "\t", stringsAsFactors = F)
    muta = read.table("Mutagenesis.txt", sep = "\t", stringsAsFactors = F)
    option = read.table("Option.txt", sep = "\t", stringsAsFactors = F)
    zoomin = read.table("ZoomIn.txt", sep = "\t", stringsAsFactors = F)
    Site = function(position, position2, name, height = -0.3, 
        x_y, up_down) {
        h1 = -0.1
        h2 = -0.2
        h = -0.4
        hh1 = -2.8
        if (up_down == "up") {
            if (position == position2) {
                segments(position, hh1 + height, position, hh1 + 
                  height + h)
            }
            else {
                segments(position, hh1 + height, position, hh1 + 
                  height + h1)
                segments(position2, hh1 + height + h - h2, position2, 
                  hh1 + height + h)
                segments(position, hh1 + height + h1, position2, 
                  hh1 + height + h - h2)
            }
            text(position2, hh1 + height + h - 0.02, name, srt = 90, 
                adj = c(0, 0.5), cex = 0.8)
        }
        else {
            if (position == position2) {
                segments(position, hh1, position, hh1 - h)
            }
            else {
                segments(position, hh1, position, hh1 - h1)
                segments(position2, hh1 - h + h2, position2, 
                  hh1 - h)
                segments(position, hh1 - h1, position2, hh1 - 
                  h + h2)
            }
            text(position2, hh1 - h + 0.02, name, srt = 270, 
                adj = c(0, 0.5), cex = 0.8)
        }
    }
    Change_x = function(site_pos, site_name, protein_width) {
        dec = 1.4 * protein_width/100
        position2 = 1:length(site_pos)
        position2[1] = site_pos[1]
        if (length(site_pos) > 1) {
            for (i in 2:length(site_pos)) {
                if (site_pos[i] - site_pos[i - 1] <= dec) {
                  if (site_pos[i] != site_pos[i - 1]) {
                    position2[i] = position2[i - 1] + dec
                  }
                  else {
                    position2[i] = position2[i - 1]
                  }
                }
                else {
                  position2[i] = site_pos[i]
                }
            }
        }
        return(position2)
    }
    if (!is.na(site[1, 1])) {
        position2 = Change_x(site[, 1], site[, 2], as.numeric(length[2]))
        for (i in 1:nrow(site)) {
            Site(position = as.numeric(site[i, 1]), position2 = position2[i], 
                name = as.character(site[i, 2]), height = as.numeric(protein[4]), 
                x_y = flag, up_down = "up")
        }
    }
  }
# }