Autoplotprotein (version 1.1)

plotdomain: ploting domain

Description

Draw the domain of the protein

Usage

plotdomain()

Value

The starting position, end position and name of the protein domain

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 domains

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)
    Domain = function(start, end, name, height = -0.3, color = "orange", 
        face = "stereoscopic", protein_width, x_y) {
        h1 = -2.8
        h2 = -3.1
        dec = 2 * nchar(name) * protein_width/100
        if (face == "stereoscopic") {
            cylindrect(start, h1, end, h2, col = color, gradient = "y")
        }
        else {
            rect(start, h1, end, h2, col = color)
        }
        if (end - start >= dec) {
            par(srt = 0)
            text((end + start)/2, h1 + height/2, name, cex = 0.7)
            isContain = TRUE
        }
        else {
            isContain = FALSE
        }
        isContain
    }
    Domain_w = function(domain_pos, domain_name, protein_width) {
        dec = 1.4 * protein_width/100
        position2 = 1:length(domain_pos)
        position2[1] = domain_pos[1]
        if (length(domain_pos) > 1) {
            for (i in 2:length(domain_pos)) {
                if (domain_pos[i] - domain_pos[i - 1] <= dec) {
                  if (domain_pos[i] != domain_pos[i - 1]) {
                    position2[i] = position2[i - 1] + dec
                  }
                  else {
                    position2[i] = position2[i - 1]
                  }
                }
                else {
                  position2[i] = domain_pos[i]
                }
            }
        }
        return(position2)
    }
    Domain_h = 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)
        }
    }
    if (!is.na(domain[1, 1])) {
        domainn = domain
        count = 0
        for (i in 1:nrow(domainn)) {
            isContain = Domain(start = as.numeric(domainn[i, 
                1]), end = as.numeric(domainn[i, 2]), name = as.character(domainn[i, 
                3]), height = as.numeric(protein[4]), color = i + 
                1, face = protein[6], protein_width = as.numeric(length[2]), 
                x_y = flag)
            if (isContain == TRUE) {
                domain = domain[-i + count, ]
                count = count + 1
            }
        }
        domain2 = (domain[, 1] + domain[, 2])/2
        if (length(domain2) != 0) {
            flag = TRUE
            if (flag == TRUE) {
                position3 = Domain_w(domain2, domain[, 3], as.numeric(length[2]))
            }
            for (i in 1:nrow(domain)) {
                position1 = (as.numeric(domain[i, 1]) + as.numeric(domain[i, 
                  2]))/2
                Domain_h(position = position1, position2 = position3[i], 
                  name = as.character(domain[i, 3]), height = as.numeric(protein[4]), 
                  x_y = flag, up_down = "down")
            }
        }
    }
  }
# }