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.customlib.r
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.customlib.r
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########################################################################
# .customlib.r
#
# Copyright (C) 2019-2020 Mahmoud M Ibrahim
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see http://www.gnu.org/licenses.
#
# Contact: [email protected] (Mahmoud M Ibrahim)
########################################################################
#custom functions
makeTransparent = function(..., alpha=0.5) {
alpha = floor(255*alpha)
newColor = col2rgb(col=unlist(list(...)), alpha=FALSE)
.makeTransparent = function(col, alpha) {
rgb(red=col[1], green=col[2], blue=col[3], alpha=alpha, maxColorValue=255)
}
newColor = apply(newColor, 2, .makeTransparent, alpha=alpha)
return(newColor)
}
color.gradient = function(x, colors=c("red","yellow","green"), colsteps=100) {
colgrad = colorRampPalette(colors, bias = 10) (colsteps) [ findInterval(x, seq(min(x),max(x), length.out=colsteps)) ]
return(colgrad)
}
legend.col = function(col, lev){
opar = par
n = length(col)
bx = par("usr")
box.cx = c(bx[2] + (bx[2] - bx[1]) / 1000,
bx[2] + (bx[2] - bx[1]) / 1000 + (bx[2] - bx[1]) / 50)
box.cy = c(bx[3], bx[3])
box.sy = (bx[4] - bx[3]) / n
xx = rep(box.cx, each = 2)
par(xpd = TRUE)
for(i in 1:n){
yy = c(box.cy[1] + (box.sy * (i - 1)),
box.cy[1] + (box.sy * (i)),
box.cy[1] + (box.sy * (i)),
box.cy[1] + (box.sy * (i - 1)))
polygon(xx, yy, col = col[i], border = col[i])
}
par(new = TRUE)
plot(0, 0, type = "n",
ylim = c(min(lev), max(lev)),
yaxt = "n", ylab = "",
xaxt = "n", xlab = "",
frame.plot = FALSE)
axis(side = 4, las = 2, tick = FALSE, line = .25)
par = opar
}
minor.ticks.axis = function(ax,n,t.ratio=0.5,mn,mx,...){
lims = par("usr")
if(ax %in%c(1,3)) lims = lims[1:2] else lims[3:4]
major.ticks = pretty(lims,n=5)
if(missing(mn)) mn = min(major.ticks)
if(missing(mx)) mx = max(major.ticks)
major.ticks = major.ticks[major.ticks >= mn & major.ticks <= mx]
labels = sapply(major.ticks,function(i) as.expression(bquote(10^ .(i))))
axis(ax,at=major.ticks,labels=labels,...)
n = n+2
minors = log10(pretty(10^major.ticks[1:2],n))-major.ticks[1]
minors = minors[-c(1,n)]
minor.ticks = c(outer(minors,major.ticks,`+`))
minor.ticks = minor.ticks[minor.ticks > mn & minor.ticks < mx]
axis(ax,at=minor.ticks,tcl=par("tcl")*t.ratio,labels=FALSE)
}
score = function(x){
x = ((x-min(x))/(max(x)-min(x)))
return(x)
}
dist2d = function(a,b,c) {
v1 = b - c
v2 = a - b
m = cbind(v1,v2)
d = abs(det(m))/sqrt(sum(v1*v1))
return(d)
}
ReadAlevin = function( base.path = NULL ){
if (! dir.exists(base.path )){
stop("Directory provided does not exist")
}
barcode.loc = paste0( base.path, "/quants_mat_rows.txt" )
gene.loc = paste0( base.path, "/quants_mat_cols.txt" )
matrix.loc = paste0( base.path, "/quants_mat.csv" )
if (!file.exists( barcode.loc )){
stop("Barcode file missing")
}
if (! file.exists(gene.loc) ){
stop("Gene name file missing")
}
if (! file.exists(matrix.loc )){
stop("Expression matrix file missing")
}
matrix <- as.matrix(read.csv( matrix.loc, header=FALSE))
matrix <- t(matrix[,1:ncol(matrix)-1])
cell.names <- readLines( barcode.loc )
gene.names <- readLines( gene.loc )
colnames(matrix) <- cell.names
rownames(matrix) <- gene.names
matrix[is.na(matrix)] <- 0
return(matrix)
}
#general color palette
col_palette = c("#d64e3c","#7dd554","#8641c6","#cfca45","#7778cb","#59803d","#d04d9c","#73d6a8","#492f60","#ccc497","#7f343b","#72acc0","#b97d40","#c796b5","#45483a","purple","green","yellow")
col_palette_trans = makeTransparent(col_palette, alpha = 0.5)
col_palette_short = c("#999999","#56B4E9","#009E73","#0072B2")
col_palette_short_trans = makeTransparent(col_palette_short, alpha = 0.4)