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Heraut Louis authored4e58b039
# \\\
# Copyright 2021-2022 Louis Héraut*1
#
# *1 INRAE, France
# louis.heraut@inrae.fr
#
# This file is part of ash R toolbox.
#
# ash R toolbox 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.
#
# ash R toolbox 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 ash R toolbox. If not, see <https://www.gnu.org/licenses/>.
# ///
#
#
# tools.R
## 1. COLOR MANAGEMENT
### 1.1. Color on colorbar ___________________________________________
# Returns a color of a palette corresponding to a value included
# between the min and the max of the variable
get_color = function (value, min, max, ncolor=256, palette_name='perso', reverse=FALSE) {
# If the value is a NA return NA color
if (is.na(value)) {
return (NA)
}
# If the palette chosen is the personal ones
if (palette_name == 'perso') {
colorList = palette_perso
# Else takes the palette corresponding to the name given
} else {
colorList = brewer.pal(11, palette_name)
}
# Gets the number of discrete colors in the palette
nSample = length(colorList)
# Recreates a continuous color palette
palette = colorRampPalette(colorList)(ncolor)
# Separates it in the middle to have a cold and a hot palette
Sample_hot = 1:(as.integer(nSample/2)+1)
Sample_cold = (as.integer(nSample/2)+1):nSample
palette_hot = colorRampPalette(colorList[Sample_hot])(ncolor)
palette_cold = colorRampPalette(colorList[Sample_cold])(ncolor)
# Reverses the palette if it needs to be
if (reverse) {
palette = rev(palette)
palette_hot = rev(palette_hot)
palette_cold = rev(palette_cold)
}
# Computes the absolute max
maxAbs = max(abs(max), abs(min))
# If the value is negative
if (value < 0) {
if (maxAbs == 0) {
idNorm = 0
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} else {
# Gets the relative position of the value in respect
# to its span
idNorm = (value + maxAbs) / maxAbs
}
# The index corresponding
id = round(idNorm*(ncolor - 1) + 1, 0)
# The associated color
color = palette_cold[id]
# Same if it is a positive value
} else {
if (maxAbs == 0) {
idNorm = 0
} else {
idNorm = value / maxAbs
}
id = round(idNorm*(ncolor - 1) + 1, 0)
color = palette_hot[id]
}
return(color)
}
### 1.2. Colorbar ____________________________________________________
# Returns the colorbar but also positions, labels and colors of some
# ticks along it
get_palette = function (min, max, ncolor=256, palette_name='perso', reverse=FALSE, nbTick=10) {
# If the value is a NA return NA color
if (is.null(min) | is.null(max)) {
return (NA)
}
# If the palette chosen is the personal ones
if (palette_name == 'perso') {
colorList = palette_perso
# Else takes the palette corresponding to the name given
} else {
colorList = brewer.pal(11, palette_name)
}
# Gets the number of discrete colors in the palette
nSample = length(colorList)
# Recreates a continuous color palette
palette = colorRampPalette(colorList)(ncolor)
# Separates it in the middle to have a cold and a hot palette
Sample_hot = 1:(as.integer(nSample/2)+1)
Sample_cold = (as.integer(nSample/2)+1):nSample
palette_hot = colorRampPalette(colorList[Sample_hot])(ncolor)
palette_cold = colorRampPalette(colorList[Sample_cold])(ncolor)
# Reverses the palette if it needs to be
if (reverse) {
palette = rev(palette)
palette_hot = rev(palette_hot)
palette_cold = rev(palette_cold)
}
# If the min and the max are below zero
if (min < 0 & max < 0) {
# The palette show is only the cold one
paletteShow = palette_cold
# If the min and the max are above zero
} else if (min > 0 & max > 0) {
# The palette show is only the hot one
paletteShow = palette_hot
# Else it is the entire palette that is shown
} else {
paletteShow = palette
}
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# The position of ticks is between 0 and 1
posTick = seq(0, 1, length.out=nbTick)
# Blank vector to store corresponding labels and colors
labTick = c()
colTick = c()
# For each tick
for (i in 1:nbTick) {
# Computes the graduation between the min and max
lab = (i-1)/(nbTick-1) * (max - min) + min
# Gets the associated color
col = get_color(lab, min=min, max=max,
ncolor=ncolor,
palette_name=palette_name,
reverse=reverse)
# Stores them
labTick = c(labTick, lab)
colTick = c(colTick, col)
}
# List of results
res = list(palette=paletteShow, posTick=posTick,
labTick=labTick, colTick=colTick)
return(res)
}
### 1.3. Palette tester ______________________________________________
# Allows to display the current personal palette
palette_tester = function (palette_name='perso', n=256) {
# If the palette chosen is the personal ones
if (palette_name == 'perso') {
colorList = palette_perso
# Else takes the palette corresponding to the name given
} else {
colorList = brewer.pal(11, palette_name)
}
# An arbitrary x vector
X = 1:n
# All the same arbitrary y position to create a colorbar
Y = rep(0, times=n)
# Recreates a continuous color palette
palette = colorRampPalette(palette_perso)(n)
# Open a plot
p = ggplot() +
# Make the theme blank
theme(
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
axis.ticks = element_blank(),
axis.line = element_blank()
) +
# Plot the palette
geom_line(aes(x=X, y=Y), color=palette[X], size=60) +
scale_y_continuous(expand=c(0, 0))
# Saves the plot
ggsave(plot=p,
filename=paste('palette_test', '.pdf', sep=''),
width=10, height=10, units='cm', dpi=100)
}
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## 2. PERSONAL PLOT __________________________________________________
### 2.1. Circle ______________________________________________________
# Allow to draw circle in ggplot2 with a radius and a center position
gg_circle = function(r, xc, yc, color="black", fill=NA, ...) {
x = xc + r*cos(seq(0, pi, length.out=100))
ymax = yc + r*sin(seq(0, pi, length.out=100))
ymin = yc + r*sin(seq(0, -pi, length.out=100))
annotate("ribbon", x=x, ymin=ymin, ymax=ymax, color=color,
fill=fill, ...)
}
## 3. NUMBER MANAGEMENT ______________________________________________
### 3.1. Number formatting ___________________________________________
# Returns the power of ten of the scientific expression of a value
get_power = function (value) {
# Do not care about the sign
value = abs(value)
# If the value is greater than one
if (value >= 1) {
# The magnitude is the number of character of integer part
# of the value minus one
power = nchar(as.character(as.integer(value))) - 1
# If value is zero
} else if (value == 0) {
# The power is zero
power = 0
# If the value is less than one
} else {
# Extract the decimal part
dec = gsub('0.', '', as.character(value), fixed=TRUE)
# Number of decimal with zero
ndec = nchar(dec)
# Number of decimal without zero
nnum = nchar(as.character(as.numeric(dec)))
# Compute the power of ten associated
power = -(ndec - nnum + 1)
}
return(power)
}
### 3.2. Pourcentage of variable _____________________________________
# Returns the value corresponding of a certain percentage of a
# data serie
gpct = function (pct, L, min_lim=NULL, shift=FALSE) {
# If no reference for the serie is given
if (is.null(min_lim)) {
# The minimum of the serie is computed
minL = min(L, na.rm=TRUE)
# If a reference is specified
} else {
# The reference is the minimum
minL = min_lim
}
# Gets the max
maxL = max(L, na.rm=TRUE)
# And the span
spanL = maxL - minL
# Computes the value corresponding to the percentage
xL = pct/100 * as.numeric(spanL)
# If the value needs to be shift by its reference
if (shift) {
xL = xL + minL
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}
return (xL)
}
### 3.3. Add months __________________________________________________
add_months = function (date, n) {
new_date = seq(date, by = paste (n, "months"), length = 2)[2]
return (new_date)
}