Autoplotprotein (version 1.1)

plotmutagensis: ploting mutagensis

Description

Draw the mutagensis of the protein

Usage

plotmutagensis()

Value

The location, height and name of the transition point

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 mutagensis

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)
    Mutagenesis = function(position, position2, color, height2, 
        height, up_down, start, end, pc, cex1) {
        h1 = -0.1
        h2 = -1.4
        h = -1.6
        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)
            }
        }
        x = 0
        kong1 = (round(log(start, 10)) + 1) * start/50
        kong2 = (round(log(end, 10)) + 1) * end/50
        if (round(log(end, 10)) + 1 <= 5) {
            kong2 = (round(log(end, 10)) + 1) * end/50
        }
        else {
            kong2 = 5 * end/50
        }
        boxplot(x, xlim = c(start - kong1, end + kong2), ylim = c(1, 
            -5.5), axes = FALSE, add = TRUE, border = FALSE)
        points(position2, height2, pch = pc, col = color, cex = cex1)
    }
    Change_h = function(muta_pos, muta_name, protein_h) {
        d = 0.1
        d1 = 0.26
        hh1 = -2.8
        height2 = 1:length(muta_pos)
        height2[1] = hh1 + protein_h - d1
        position_h = muta_pos
        position_h[1] = muta_pos[1]
        if (length(muta_pos) > 1) {
            for (i in 2:length(muta_pos)) {
                if (muta_pos[i] == position_h[i - 1]) {
                  height2[i] = height2[i - 1] - d
                }
                else {
                  height2[i] = hh1 + protein_h - d1
                }
            }
        }
        height2
    }
    Change_m = function(muta, protein_width) {
        dec = 1.4 * protein_width/100
        position3 = 1:length(muta)
        position3[1] = muta[1]
        if (length(muta) > 1) {
            for (i in 2:length(muta)) {
                if (muta[i] - muta[i - 1] <= dec) {
                  if (muta[i] != muta[i - 1]) {
                    position3[i] = position3[i - 1] + dec
                  }
                  else {
                    position3[i] = position3[i - 1]
                  }
                }
                else {
                  position3[i] = muta[i]
                }
            }
        }
        position3
    }
    if (!is.na(muta[1, 1])) {
        position3 = Change_m(muta[, 1], as.numeric(length[2]))
        height2 = Change_h(muta[, 1], muta[, 2], as.numeric(protein[4]))
        for (i in 1:nrow(muta)) {
            Mutagenesis(position = as.numeric(muta[i, 1]), position2 = position3[i], 
                color = as.character(muta[i, 2]), height2 = height2[i], 
                height = as.numeric(protein[4]), up_down = "up", 
                start = as.numeric(length[1]), end = as.numeric(length[2]), 
                pc = as.numeric(protein[7]), cex1 = as.numeric(protein[8]))
        }
    }
  }
# }