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ngs_R_function.R
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##################################################################################################################################
# Data 2019-08-03
# Author Howard MENG
# E-mail [email protected]
# useful R function
##################################################################################################################################
#------------------------------------------------------------------------------------------>>>>>>>
# contents
#------------------------------------------------------------------------------------------>>>>>>>
# plot.TAD function for plot Hi-C TAD
# plot.matrix easy to plot heatmap
#------------------------------------------------------------------------------------------>>>>>>>
# function part
#------------------------------------------------------------------------------------------>>>>>>>
plot.TAD <- function(input.matrix,col.min = "red",col.max = "red",col.boundary = 0,ylim=NULL,minBound=0,maxBound=0.95,mat.upper=T,mat.part=T){
# 参数说明
## input.matrix: 输入矩阵
## col.min="red": 热图颜色，支持字符或者是RGB参数za
## col.max="red": 热图颜色，支持字符或者是RGB参数
## col.boundary=0: 两种颜色的分界线，也即白色对应的值
## ylim=NULL: 热图的y轴范围，1个bin的长度是1，方便截短
## minBound=0: 使用分位数来修正最小值
## maxBound=0.95: 使用分位数修正最大值，默认matrix中的95%分位数为最大值
## mat.upper=T: 如果为TRUE画上半部分，为FALSE画下半部分; 只有在mat.part=T时有效
## mat.part=T: 如果为TRUE则画三角，如果为FLASE则画倒置的matrix
input.matrix = as.matrix(input.matrix)
mat.nrow = dim(input.matrix)[1]
## color type 1：single color
## color type 2：blue white red black
## 生成矩阵需要的颜色
mat.lower.tri = as.vector(input.matrix[lower.tri(input.matrix,diag = F)])
mat.quantile = quantile(as.vector(input.matrix[lower.tri(input.matrix,diag = T)]),prob=c(minBound,maxBound))
if(col.boundary>mat.quantile[2] | col.boundary<mat.quantile[1]){
print("Error! col.boundary have to smaller than matrix maxBound value!")
return(NULL)
}
## fix value,too large or too small
mat.lower.tri[mat.lower.tri < mat.quantile[1]] = mat.quantile[1]
mat.lower.tri[mat.lower.tri > mat.quantile[2]] = mat.quantile[2]
mat.diagnal.value = diag(input.matrix)
mat.diagnal.value[mat.diagnal.value < mat.quantile[1]] = mat.quantile[1]
mat.diagnal.value[mat.diagnal.value > mat.quantile[2]] = mat.quantile[2]
## create color vector
mat.lower.tri.col_alpha = rep(0,length(mat.lower.tri))
mat.diagnal.col_alpha = rep(0,length(mat.diagnal.value))
mat.lower.tri.col_alpha[mat.lower.tri>=col.boundary] = ceiling((mat.lower.tri[mat.lower.tri>=col.boundary] - col.boundary) / (mat.quantile[2] - col.boundary) * 255)
mat.lower.tri.col_alpha[mat.lower.tri<col.boundary] = ceiling((col.boundary - mat.lower.tri[mat.lower.tri<col.boundary]) / (col.boundary - mat.quantile[1]) * 255)
mat.diagnal.col_alpha[mat.diagnal.value>=col.boundary] = ceiling((mat.diagnal.value[mat.diagnal.value>=col.boundary] - col.boundary) / (mat.quantile[2] - col.boundary) * 255)
mat.diagnal.col_alpha[mat.diagnal.value<col.boundary] = ceiling((col.boundary - mat.diagnal.value[mat.diagnal.value<col.boundary]) / (col.boundary - mat.quantile[1]) * 255)
mat.lower.tri.color = rep("##FFFFFF",length(mat.lower.tri))
mat.diagnal.color = rep("##FFFFFF",length(mat.diagnal.value))
mat.lower.tri.color[mat.lower.tri>=col.boundary] = rgb(t(col2rgb(col.max)),alpha = mat.lower.tri.col_alpha[mat.lower.tri>=col.boundary],maxColorValue = 255)
mat.lower.tri.color[mat.lower.tri<col.boundary] = rgb(t(col2rgb(col.min)),alpha = mat.lower.tri.col_alpha[mat.lower.tri<col.boundary],maxColorValue = 255)
mat.diagnal.color[mat.diagnal.value>=col.boundary] = rgb(t(col2rgb(col.max)),alpha = mat.diagnal.col_alpha[mat.diagnal.value>=col.boundary],maxColorValue = 255)
mat.diagnal.color[mat.diagnal.value<col.boundary] = rgb(t(col2rgb(col.min)),alpha = mat.diagnal.col_alpha[mat.diagnal.value<col.boundary],maxColorValue = 255)
# 根据矩阵的行列，生成x1,y1的坐标
x1.part = c(1:(mat.nrow -1))
y1.part = c(1:(mat.nrow -1))
x1 = x1.part
y1 = y1.part
for(i in c(1:(mat.nrow-1))){
x1.part = x1.part[-length(x1.part)] + 2
y1.part = y1.part[-length(y1.part)]
x1 = c(x1,x1.part)
y1 = c(y1,y1.part)
}
# 对角线的x1
x1.diagonal = c(0:(mat.nrow-1)) * 2
y1.diagonal = rep(0,mat.nrow)
if(mat.part==T){
# plot matrix upper OR lower only.
x1 = c(x1,x1.diagonal)
y1 = c(y1,y1.diagonal)
# 颜色向量也不同
mat.color = c(mat.lower.tri.color,mat.diagnal.color)
}else if(mat.part==F){
x1 = c(x1,x1.diagonal,x1)
y1 = c(y1,y1.diagonal,-y1)
mat.color = c(mat.lower.tri.color,mat.diagnal.color,mat.lower.tri.color)
}
# 根据x1 y1 生成剩余坐标
x2 = x1 + 1
x3 = x2 + 1
x4 = x2
y2 = y1 + 1
y3 = y1
y4 = y1 - 1
# 需要按照x1,x2,x3,x4,NA的格式进行生成x vector否则会把所有的点连在一起
NA_vector = rep(NA,length(x1))
# 生成按照x11,x12,x13,x14,NA,x21,x22,x23,x24,NA...排列的x与y
x_matrix = matrix(c(x1,x2,x3,x4,NA_vector),ncol = 5)
y_matrix = matrix(c(y1,y2,y3,y4,NA_vector),ncol = 5)
x = as.vector(t(x_matrix))
y = as.vector(t(y_matrix))
# 绘图部分
## 如果mat.upper 为F 则画倒置的图像
## 设置画布大小
x.point = c(0,mat.nrow*2)
if(mat.part){
if(! mat.upper){ y = -y ; y.point = c(-mat.nrow,1)}else{ y.point = c(-1,mat.nrow) }
}else{
y.point = c(-mat.nrow,mat.nrow)
}
## 设置ylim
if(is.null(ylim)){ ylim = y.point }
## 生成画布
plot(x.point,y.point,ylim=ylim,type="n",frame.plot =F,xaxt="n",yaxt="n",xlab="",ylab="")
## 画三角矩阵
polygon(x,y,col = mat.color,border = F)
}
plot.matrix <- function(mat,bound.min=0,bound.max=1,mat.lim=NULL,color_type=1,col.min = "red",col.max = "red",col.boundary = NULL){
# mat = hic matrix
# min_bound min quantile to miss data
# max_bound max quantile to miss data
mat <- as.matrix(mat)
#matrix info calculate
row_num <- dim(mat)[1]
col_num <- dim(mat)[2]
#matrix rects' coordinate
x1 <- rep(c(0:(col_num-1)),each=row_num)
x2 <- x1 + 1
y1 <- rep(c(0:(-row_num+1)),col_num)
y2 <- y1 -1
#matrix colour vector
if(color_type == 1){
## 生成矩阵需要的颜色
###确定 matrix的上下界
mat.quantile = quantile(as.vector(mat),prob=c(bound.min,bound.max))
if(is.null(mat.lim)){
mat.lim = mat.quantile
}else{
mat.lim = c(min(c(mat.quantile,mat.lim)),max(c(mat.quantile,mat.lim)))
}
if(is.null(col.boundary)){
col.boundary = mat.lim[1]
}
if(col.boundary>mat.lim[2]){
print("Error! col.boundary have to smaller than matrix mat.lim[2] value!")
return(NULL)
}else if(col.boundary<mat.lim[1]){
print("Error! col.boundary have to larger than matrix mat.lim[1] value!")
print(mat.lim)
print(col.boundary)
return(NULL)
}
## fix value,too large or too small
mat[mat < mat.lim[1]] = mat.lim[1]
mat[mat > mat.lim[2]] = mat.lim[2]
## create color vector
mat.col_alpha = rep(0,length(as.vector(mat)))
mat.col_alpha[mat >= col.boundary] = ceiling((mat[mat >= col.boundary] - col.boundary) / (mat.lim[2] - col.boundary) * 255)
mat.col_alpha[mat < col.boundary] = ceiling((col.boundary - mat[mat < col.boundary]) / (col.boundary - mat.lim[1]) * 255)
mat.color = rep("#FFFFFF",length(as.vector(mat)))
mat.color[mat>=col.boundary] = rgb(t(col2rgb(col.max)),alpha = mat.col_alpha[mat>=col.boundary],maxColorValue = 255)
mat.color[mat< col.boundary] = rgb(t(col2rgb(col.min)),alpha = mat.col_alpha[mat< col.boundary],maxColorValue = 255)
}else if(color_type == 2){
# input a col_list
}
# plot the final matrix
plot(x=c(0,col_num),y=c(-row_num,0),type="n",frame.plot = F,xaxt="n",yaxt="n",cex.main = 2,xlab="",ylab="")
rect(x1,y1,x2,y2,col = mat.color,border = NA)
}
#------------------------------------------------------------------------------------------>>>>>>>
# MIT License
#------------------------------------------------------------------------------------------>>>>>>>
# Copyright (c) 2019 MENG Howard
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# 2019-08-03 By MENG