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tools.R 9.20 KiB
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# \\\
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# Copyright 2021-2022 Louis Héraut*1
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#
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# *1   INRAE, France
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#      louis.heraut@inrae.fr
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#
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# This file is part of ash R toolbox.
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#
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# ash R toolbox is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or (at
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# your option) any later version.
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#
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# ash R toolbox is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
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# General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with ash R toolbox.  If not, see <https://www.gnu.org/licenses/>.
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# ///
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#
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#
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# tools.R
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## 1. COLOR MANAGEMENT
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### 1.1. Color on colorbar ___________________________________________
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# Returns a color of a palette corresponding to a value included
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# between the min and the max of the variable
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get_color = function (value, min, max, ncolor=256, palette_name='perso', reverse=FALSE) {
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    # If the value is a NA return NA color
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    if (is.na(value)) {
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        return (NA)
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    }
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    # If the palette chosen is the personal ones
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    if (palette_name == 'perso') {
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        colorList = palette_perso
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    # Else takes the palette corresponding to the name given
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    } else {
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        colorList = brewer.pal(11, palette_name)
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    }
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    # Gets the number of discrete colors in the palette
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    nSample = length(colorList)
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    # Recreates a continuous color palette
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    palette = colorRampPalette(colorList)(ncolor)
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    # Separates it in the middle to have a cold and a hot palette
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    Sample_hot = 1:(as.integer(nSample/2)+1)
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    Sample_cold = (as.integer(nSample/2)+1):nSample
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    palette_hot = colorRampPalette(colorList[Sample_hot])(ncolor)
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    palette_cold = colorRampPalette(colorList[Sample_cold])(ncolor)
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    # Reverses the palette if it needs to be
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    if (reverse) {
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        palette = rev(palette)
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        palette_hot = rev(palette_hot)
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        palette_cold = rev(palette_cold)
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    }
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    # Computes the absolute max
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    maxAbs = max(abs(max), abs(min))
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    # If the value is negative
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    if (value < 0) {
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        if (maxAbs == 0) {
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            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) }