| Type: | Package |
| Title: | Development of Visualization Tools for Protein Sequence |
| Version: | 1.1 |
| Date: | 2017-06-02 |
| Author: | Xiaoyu Zhang |
| Maintainer: | Yao Geng <gengyao0103521@qq.com> |
| Description: | The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed. |
| License: | GPL-3 |
| Depends: | XML, plyr, plotrix, seqinr, ade4 |
| NeedsCompilation: | no |
| Packaged: | 2017-07-06 01:05:04 UTC; Administrator |
| Repository: | CRAN |
| Date/Publication: | 2017-07-06 10:00:07 UTC |
Development of Visualization Tools for Protein Sequence
Description
The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed.
Details
The DESCRIPTION file:
| Package: | Autoplotprotein |
| Type: | Package |
| Title: | Development of Visualization Tools for Protein Sequence |
| Version: | 1.1 |
| Date: | 2017-06-02 |
| Author: | Xiaoyu Zhang |
| Maintainer: | Yao Geng <gengyao0103521@qq.com> |
| Description: | The image of the amino acid transform on the protein level is drawn, and the automatic routing of the functional elements such as the domain and the mutation site is completed. |
| License: | GPL-3 |
| Depends: | XML, plyr, plotrix, seqinr, ade4 |
Index of help topics:
Autoplotprotein Two - dimensional structure of protein
Autoplotprotein-package
Development of Visualization Tools for Protein
Sequence
conservation conservation
data Save the information
domain_data downloading protein length
length_data downloading protein length
plotdomain ploting domain
plotmutagensis ploting mutagensis
plotsite ploting site
site_data downloading protein site
Author(s)
Xiaoyu Zhang
Maintainer: Yao Geng <gengyao0103521@qq.com>
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Two - dimensional structure of protein
Description
Draw a visualized structure of the protein
Usage
Autoplotprotein()
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
Value
Visualization of protein structure
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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 ()
{
library("ade4")
library("seqinr")
library("plotrix")
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)
size <- c(10.5, 7.27)
high <- c(1, -1)
sizen = size[1]
highn = high[1]
if (option[2, 2] == "no") {
sizen = size[2]
highn = high[2]
}
path = protein[1]
pdf(as.character(path), height = sizen[1], width = 11)
layout(matrix(c(1, 2), nrow = 1), widths = c(1, 3))
par(oma = c(3, 0, 2, 0), mar = c(4, 0, 2, 0) + 0.4)
nameOfYourQuery = option[2, 1]
additionalOptions = option[2, 2]
showReferenceSequence = option[2, 3]
showConservationScore = option[2, 4]
showGridlinesAtTicks = option[2, 5]
conservation = option[2, 6]
zoomIn = zoomin[2, 1]
zoomStart = zoomin[2, 2]
zoomEnd = zoomin[2, 3]
tickSize = as.numeric(zoomin[2, 4])
plot((-30:-15), rep(-1, 16), col = "white", type = "l", ann = FALSE,
bty = "n", xaxt = "n", yaxt = "n", xlim = c(-160, -15),
ylim = c(highn[1], -5.5))
if (additionalOptions == "yes") {
if (conservation == "yes") {
lines((-30:-15), rep(0, 16), col = "purple3")
lines((-30:-15), rep(-0.5, 16), col = "purple3")
lines((-30:-15), rep(-1, 16), col = "purple3")
text(-100, -0.5, "Conservation", col = "purple3",
cex = 0.9, font = 2)
text(-45, -1, "1", col = "purple3", cex = 0.9)
text(-45, -0.5, "0.5", col = "purple3", cex = 0.9)
text(-45, 0, "0", col = "purple3", cex = 0.9)
}
}
if (additionalOptions == "yes") {
if (showReferenceSequence == "yes") {
text(-100, -4.9, "Reference", col = "black", cex = 0.9,
font = 2)
}
}
if (additionalOptions == "yes") {
if (showConservationScore == "yes") {
text(-100, 0.5, "Score", col = "purple3", cex = 0.9,
font = 2)
}
}
text(-100, -2.95, nameOfYourQuery, col = "blue", cex = 0.9,
font = 2)
Protein = function(start = 1, end, height = -0.3, color = "green",
face = "stereoscopic") {
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
}
h1 = -2.8
h2 = -3.1
boxplot((1:as.numeric(end)), rep(h1, as.numeric(end)),
xlab = "Amino Acid Position", ylab = "", xlim = c(0,
as.numeric(end)), ylim = c(highn[1], -5.5), axes = FALSE)
if (face == "stereoscopic") {
cylindrect(start, h1, end, h2, col = color, gradient = "y")
}
else {
rect(start, h1, end, h2, col = color)
}
text(0, h1 - height/2, start, adj = 1)
text(end - 17, h1 - height/2, end, adj = 0)
}
ZoomIn = function(start = 1, end, height = -0.3, color = "green",
face = "stereoscopic", zoomstart, zoomend) {
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
}
h1 = -2.8
h2 = -3.1
boxplot((as.numeric(zoomstart):as.numeric(zoomend)),
rep(h1, as.numeric(zoomend)), xlab = "Amino Acid Position",
ylab = "", xlim = c(as.numeric(zoomstart), as.numeric(zoomend)),
ylim = c(highn[1], -5.5), axes = FALSE)
if (face == "stereoscopic") {
cylindrect(start, h1, end, h2, col = color, gradient = "y")
}
else {
rect(start, h1, end, h2, col = color)
}
text(start, h1 + height/2, start, adj = 1)
text(end, h1 + height/2, end, adj = 0)
}
if (zoomIn == "yes") {
ZoomIn(start = as.numeric(length[1]), end = as.numeric(length[2]),
height = as.numeric(protein[4]), color = as.character(protein[5]),
face = protein[6], zoomstart = zoomin[2, 2], zoomend = zoomin[2,
3])
}
else {
Protein(start = as.numeric(length[1]), end = as.numeric(length[2]),
height = as.numeric(protein[4]), color = as.character(protein[5]),
face = protein[6])
}
legend("topleft", legend = c("mutation", "Protein Domain"),
pch = c(19, 15), col = c("lightseagreen", "deeppink"),
box.col = "white", bg = "white", pt.cex = 1.5, text.width = 1)
ticks = seq(0, as.numeric(length[2]), by = tickSize)
axis(side = 1, at = ticks, las = 3)
if (additionalOptions == "yes") {
if (showGridlinesAtTicks == "yes") {
len = array(rep(1:as.numeric(length[2])))
for (i in 1:length(len)) {
abline(v = ticks[i], lty = 3, lwd = 0.5, col = "lightgray")
}
}
}
}
conservation
Description
Draw a conservative curve, calculate the conservative score
Usage
conservation()
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 includeting conservation, conservation score
Value
The returned value is a conservative score
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
Examples
##---- 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)
nameOfYourQuery = option[2, 1]
additionalOptions = option[2, 2]
showReferenceSequence = option[2, 3]
showConservationScore = option[2, 4]
showGridlinesAtTicks = option[2, 5]
conservation = option[2, 6]
zoomIn = zoomin[2, 1]
zoomStart = zoomin[2, 2]
zoomEnd = zoomin[2, 3]
tickSize = as.numeric(zoomin[2, 4])
referenceSequencePositionInFile = option[2, 7]
option = read.table("Option.txt", sep = "\t", stringsAsFactors = F)
a <- read.fasta(file = "alignmentFile.fasta")
seq <- list()
for (i in 1:length(a)) {
seq[[i]] <- a[[i]][1:length(a[[i]])]
}
numberOfSeq <- length(seq)
mat <- matrix(0, nrow = length(a), ncol = length(a[[1]]))
for (i in 1:length(seq)) {
mat[i, ] <- seq[[i]]
}
df <- as.data.frame(mat)
tdf <- t(df)
referenceSequencePositionInFile = option[2, 7]
referenceSeq <- tdf[which(tdf[, as.numeric(referenceSequencePositionInFile)] !=
"-"), ]
referenceSeq <- as.data.frame(referenceSeq)
write.table(referenceSeq, file = "alignment_table", sep = "\t",
quote = F, row.names = F, col.names = F)
counter <- rep(0, nrow(referenceSeq))
a <- read.table("alignment_table", sep = "\t")
a <- data.frame(lapply(a, as.character), stringsAsFactors = FALSE)
for (i in 1:nrow(a)) {
a[i, "consensus"] <- paste(as.character(a[i, ]), collapse = "")
}
countBases <- function(string) {
table(strsplit(string, "")[[1]])
}
c <- as.character(a[, "consensus"])
tab <- list()
for (i in 1:length(c)) {
tab[[i]] <- countBases(c[i])
}
score <- rep(0, nrow(a))
for (i in 1:length(tab)) {
for (j in 1:length(tab[[i]])) {
if ((names(tab[[i]][j])) == a[i, ][as.numeric(referenceSequencePositionInFile)])
score[i] <- tab[[i]][j]
}
}
scorePlot <- -(((score/numberOfSeq)))
a <- read.fasta(file = "alignmentFile.fasta")
seqForPlot <- a[[as.numeric(referenceSequencePositionInFile)]][
which(a[[as.numeric(referenceSequencePositionInFile)]] !=
"-")]
if (additionalOptions == "yes") {
if (conservation == "yes") {
lines(scorePlot, col = "purple3")
}
}
if (additionalOptions == "yes") {
if (showReferenceSequence == "yes") {
rect(0, -4.75, length(scorePlot), -5.05, col = "white",
border = NA)
for (i in 1:length(seqForPlot)) {
text(i, -4.9, toupper(seqForPlot[i]), font = 2,
cex = 1)
}
}
}
if (additionalOptions == "yes") {
if (showConservationScore == "yes") {
rect(0, 0.3, length(scorePlot), 0.7, col = "white",
border = NA)
for (i in 1:length(seqForPlot)) {
text(i, 0.5, toupper(abs(round(scorePlot[i],
1))), font = 2, cex = 0.8, srt = 90, col = "purple3")
}
}
}
}
Save the information
Description
Keep all the information of the painted protein in a file
Usage
data()
Details
Save information, including protein mutation point information, domain information, option information, enlargement information, protein information, length information and site information
Value
Data of various kinds of information
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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 ()
{
library("ade4")
library("seqinr")
library("plotrix")
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)
c <- merge(muta, domain, all = T, sort = FALSE)
c <- merge(c, option, all = T, sort = FALSE)
c <- merge(c, zoomin, all = T, sort = FALSE)
c <- merge(c, protein, all = T, sort = FALSE)
c <- merge(c, length, all = T, sort = FALSE)
c <- merge(c, site, all = T, sort = FALSE)
write.table(c, file = "data.txt", sep = "\t", quote = FALSE,
row.names = F, col.names = F)
}
downloading protein length
Description
Load the start and end positions of the domain
Usage
domain_data()
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
Value
The start and end positions of the domain
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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 ()
{
library(XML)
library(plyr)
protein = read.table("Protein.txt", sep = "\t", stringsAsFactors = F)
name = protein[2]
url_p = "http://www.uniprot.org/uniprot/"
url_s = "#showFeatures"
url_w = paste(url_p, name, url_s, sep = "")
url = url_w
doc <- htmlParse(url)
position_d = xpathSApply (doc, "//table[@id= 'domainsAnno_section']
/tr/td/ a[@class = 'position tooltipped']",
xmlValue)
name_d = xpathSApply (doc, "//table[@id= 'domainsAnno_section']/tr/td/span[@property='text']",
xmlValue)
s_d = c()
for (i in 1:length(position_d)) {
s_d[i] <- gsub(pattern = "//D", replacement = "x", position_d[i])
}
s_d <- strsplit(s_d, "xxx")
d1_d <- laply(s_d, function(x) x[1])
d2_d <- laply(s_d, function(x) x[2])
r1_d = d1_d
r2_d = d2_d
r3_d = name_d
dfrm_d = data.frame(r1_d, r2_d, r3_d)
write.table(dfrm_d, file = "Domain.txt", sep = "/t", quote = FALSE,
row.names = F, col.names = F)
}
downloading protein length
Description
Download the length of the protein, including the starting and ending positions
Usage
length_data()
Details
Download the length of the protein, including the starting and ending positions
Value
The length of the protein
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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 ()
{
library(XML)
library(plyr)
protein = read.table("Protein.txt", sep = "\t", stringsAsFactors = F)
name = protein[2]
url_p = "http://www.uniprot.org/uniprot/"
url_s = "#showFeatures"
url_w = paste(url_p, name, url_s, sep = "")
url = url_w
doc <- htmlParse(url)
position_l = xpathSApply (doc, "//table[@id= 'peptides_section']
/tr/td/ a[@class = 'position tooltipped']",
xmlValue)
s_l <- c()
for (i in 1:length(position_l)) {
s_l[i] <- gsub(pattern = "//D", replacement = "x", position_l[i])
}
s_l <- strsplit(s_l, "xxx")
d2_l <- laply(s_l, function(x) x[2])
r1_l <- 0
r2_l <- d2_l
dfrm_l <- data.frame(r1_l, r2_l)
write.table(dfrm_l, file = "Length.txt", sep = "/t", quote = FALSE,
row.names = F, col.names = F)
}
ploting domain
Description
Draw the domain of the protein
Usage
plotdomain()
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
Value
The starting position, end position and name of the protein domain
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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")
}
}
}
}
ploting mutagensis
Description
Draw the mutagensis of the protein
Usage
plotmutagensis()
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
Value
The location, height and name of the transition point
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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]))
}
}
}
ploting site
Description
Draw the protein site
Usage
plotsite()
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
Value
Location of the site in the protein
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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")
}
}
}
downloading protein site
Description
Download the site of the protein, including the name
Usage
site_data()
Details
Download the site of the protein, including the distribution of the locus of the marker space
Value
The location of the marker line
Author(s)
Xiaoyu Zhang
References
https://cran.r-project.org/doc/manuals/R-exts.html
See Also
codehelp
Examples
##---- 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 ()
{
library(XML)
library(plyr)
protein = read.table("Protein.txt", sep = "\t", stringsAsFactors = F)
name = protein[2]
url_p = "http://www.uniprot.org/uniprot/"
url_s = "#showFeatures"
url_w = paste(url_p, name, url_s, sep = "")
url = url_w
doc <- htmlParse(url)
position_s = xpathSApply (doc, "//table[@id= 'sitesAnno_section']
/tr/td/ a[@class = 'position tooltipped']",
xmlValue)
name_s = xpathSApply (doc, "//table[@id= 'sitesAnno_section']/tr/td/span[@property='text']",
xmlValue)
s_s <- c()
for (i in 1:length(position_s)) {
s_s[i] <- gsub(pattern = "//D", replacement = "x", position_s[i])
}
s_s <- strsplit(s_s, "xxx")
d1_s <- laply(s_s, function(x) x[1])
d2_s <- laply(s_s, function(x) x[2])
r1_site = d1_s
r2_site = name_s
dfrm_site = data.frame(r1_site, r2_site)
write.table(dfrm_site, file = "Site.txt", sep = "/t", quote = FALSE,
row.names = F, col.names = F)
}