layout.R

# \\\
# Copyright 2021-2022 Louis Hraut*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/>.
# ///
#
#
# plotting/layout.R
#
#


# Usefull library
library(ggplot2)
library(scales)
library(qpdf)
library(gridExtra)
library(gridtext)
library(dplyr)
library(grid)
library(ggh4x)
library(RColorBrewer)
library(rgdal)
library(shadowtext)

# Sourcing R file
source('plotting/time.R', encoding='latin1')
source('plotting/info.R', encoding='latin1')
source('plotting/map.R', encoding='latin1')
source('plotting/matrix.R', encoding='latin1')
source('plotting/other.R', encoding='latin1')


## 1. PERSONALISATION
### 1.1. Personal theme
theme_ash =
    theme(
        # White background
        panel.background=element_rect(fill='white'),
        # Font
        text=element_text(family='sans'),
        # Border of plot
        panel.border = element_rect(color="grey85",
                                    fill=NA,
                                    size=0.7),
        # Grid
        panel.grid.major.x=element_blank(),
        panel.grid.major.y=element_blank(),
        # Ticks marker
        axis.ticks.x=element_line(color='grey75', size=0.3),
        axis.ticks.y=element_line(color='grey75', size=0.3),
        # Ticks label
        axis.text.x=element_text(color='grey40'),
        axis.text.y=element_text(color='grey40'),
        # Ticks length
        axis.ticks.length=unit(1.5, 'mm'),
        # Ticks minor
        ggh4x.axis.ticks.length.minor=rel(0.5),
        # Title
        plot.title=element_text(size=9, vjust=-2, 
                                hjust=-1E-3, color='grey20'), 
        # Axis title
        axis.title.x=element_blank(),
        axis.title.y=element_blank(),
        # Axis line
        axis.line.x=element_blank(),
        axis.line.y=element_blank(),
        )

### 1.2. Color palette
palette_perso = c('#0f3b57',
                  '#1d7881',
                  '#80c4a9',
                  '#e2dac6', #mid
                  '#fadfad',
                  '#d08363',
                  '#7e392f')


## 2. LAYOUT
datasheet_layout = function (df_data, df_meta, layout_matrix, isplot=c('datasheet', 'matrix', 'map'), figdir='', filedir_opt='', filename_opt='', variable='', df_trend=NULL, p_threshold=0.1, unit2day=365.25, type='', trend_period=NULL, mean_period=NULL, axis_xlim=NULL, missRect=FALSE, time_header=NULL, info_header=TRUE, info_ratio=1, time_ratio=2, var_ratio=3, df_shapefile=NULL) {
    
    outfile = "Panels"
    if (filename_opt != '') {
        outfile = paste(outfile, '_', filename_opt, sep='')
    }
    outfile = paste(outfile, '.pdf', sep='')

    # If there is not a dedicated figure directory it creats one
    outdir = file.path(figdir, filedir_opt, sep='')
    if (!(file.exists(outdir))) {
        dir.create(outdir)
    }

    outdirTmp = file.path(outdir, 'tmp')
    if (!(file.exists(outdirTmp))) {
        dir.create(outdirTmp)
    } else {
        unlink(outdirTmp, recursive=TRUE)
        dir.create(outdirTmp)
    }

    nbp = length(df_data)

    if (all(class(df_data) != 'list')) {
        df_data = list(df_data)
    }

    if (all(class(df_trend) != 'list')) {
        df_trend = list(df_trend)
        if (length(df_trend) == 1) {
            df_trend = replicate(nbp, df_trend)
        }}

    if (all(class(p_threshold) != 'list')) {
        p_threshold = list(p_threshold)
        if (length(p_threshold) == 1) {
            p_threshold = replicate(nbp, p_threshold)
        }}
  
    if (all(class(unit2day) != 'list')) {
        unit2day = list(unit2day)
        if (length(unit2day) == 1) {
            unit2day = replicate(nbp, unit2day)
        }}

    if (all(class(type) != 'list')) {
        type = list(type)
        if (length(type) == 1) {
            type = replicate(nbp, type)
        }}

    if (all(class(missRect) != 'list')) {
        missRect = list(missRect)
        if (length(missRect) == 1) {
            missRect = replicate(nbp, missRect)
        }}

    list_df2plot = vector(mode='list', length=nbp)
    # minTrend = c()
    # maxTrend = c()

    for (i in 1:nbp) {
        
        df2plot = list(data=df_data[[i]], 
                       trend=df_trend[[i]],
                       p_threshold=p_threshold[[i]],
                       unit2day=unit2day[[i]],
                       type=type[[i]],
                       missRect=missRect[[i]])
        
        # okTrend = df_trend[[i]]$trend[df_trend[[i]]$p <= p_threshold[[i]]]

        # minTrend[i] = min(okTrend, na.rm=TRUE)
        # maxTrend[i] = max(okTrend, na.rm=TRUE)

        list_df2plot[[i]] = df2plot
    }


    if ('datasheet' %in% isplot) {
        time_panel(list_df2plot, df_meta, trend_period, info_header=info_header, time_header=time_header, layout_matrix=layout_matrix, info_ratio=info_ratio, time_ratio=time_ratio, var_ratio=var_ratio, outdirTmp=outdirTmp)
    }


    if ('matrix' %in% isplot) {
        matrix_panel(list_df2plot, df_meta, trend_period, mean_period,
                      slice=12, outdirTmp=outdirTmp, A3=TRUE)
    }
    
    if ('map' %in% isplot) {
        map_panel(list_df2plot, 
                  df_meta,
                  idPer=length(trend_period),
                  df_shapefile=df_shapefile,
                  outdirTmp=outdirTmp,
                  margin=margin(t=5, r=0, b=5, l=5, unit="mm"))
    }
    
    # PDF combine
    pdf_combine(input=file.path(outdirTmp, list.files(outdirTmp)),
                output=file.path(outdir, outfile))
    # unlink(outdirTmp, recursive=TRUE)
} 


## 3. COLOR MANAGEMENT
### 3.1. Color on colorbar
get_color = function (value, min, max, ncolor=256, palette_name='perso', reverse=FALSE) {
    
    if (palette_name == 'perso') {
        colorList = palette_perso
    } else {
        colorList = brewer.pal(11, palette_name)
    }
    
    nSample = length(colorList)
    
    palette = colorRampPalette(colorList)(ncolor)
    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)

    if (reverse) {
        palette = rev(palette)
        palette_hot = rev(palette_hot)
        palette_cold = rev(palette_cold)
    }

    if (is.na(value)) {
        return (NA)
    }

    maxAbs = max(abs(max), abs(min))
    
    if (value < 0) {
        idNorm = (value + maxAbs) / maxAbs
        id = round(idNorm*(ncolor - 1) + 1, 0)
        color = palette_cold[id]
    } else {
        idNorm = value / maxAbs
        id = round(idNorm*(ncolor - 1) + 1, 0)
        color = palette_hot[id]
    }
    
    return(color)
}

### 3.2. Colorbar
get_palette = function (min, max, ncolor=256, palette_name='perso', reverse=FALSE, nbTick=10) {
    
    if (palette_name == 'perso') {
        colorList = palette_perso
    } else {
        colorList = brewer.pal(11, palette_name)
    }
    
    nSample = length(colorList)
    
    palette = colorRampPalette(colorList)(ncolor)
    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)

    if (reverse) {
        palette = rev(palette)
        palette_hot = rev(palette_hot)
        palette_cold = rev(palette_cold)
    }  

    if (min < 0 & max < 0) {
        paletteShow = palette_cold
    } else if (min > 0 & max > 0) {
        paletteShow = palette_hot
    } else {
        paletteShow = palette
    }

    posTick = seq(0, 1, length.out=nbTick)
    
    labTick = c()
    colTick = c()
    for (i in 1:nbTick) {
        lab = (i-1)/(nbTick-1) * (max - min) + min
        labTick = c(labTick, lab)
        col = get_color(lab, min=min, max=max,
                        ncolor=ncolor,
                        palette_name=palette_name,
                        reverse=reverse)
            colTick = c(colTick, col)
    }
    
    return(list(palette=paletteShow, posTick=posTick,
                labTick=labTick, colTick=colTick))
}

### 3.3. Palette tester 
palette_tester = function (n=256) {

    X = 1:n
    Y = rep(0, times=n)

    palette = colorRampPalette(palette_perso)(n)

    p = ggplot() + 

    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()
    ) +
    
        geom_line(aes(x=X, y=Y), color=palette[X], size=60) +
        scale_y_continuous(expand=c(0, 0))
    
    ggsave(plot=p,
           filename=paste('palette_test', '.pdf', sep=''),
           width=10, height=10, units='cm', dpi=100)
}


## 4. OTHER
### 4.1. Number formatting
get_power = function (value) {
    
    if (value > 1) {
        power = nchar(as.character(as.integer(value))) - 1
    } else {
        dec = gsub('0.', '', as.character(value), fixed=TRUE)
        ndec = nchar(dec)
        nnum = nchar(as.character(as.numeric(dec)))
        power = -(ndec - nnum + 1)
    }
    
    return(power)
}

### 4.2. Pourcentage of variable
gpct = function (pct, L, ref=NULL, shift=FALSE) {
    
    if (is.null(ref)) {
        minL = min(L, na.rm=TRUE)
    } else {
        minL = ref
    }
    
    maxL = max(L, na.rm=TRUE)
    spanL = maxL - minL
    
    xL = pct/100 * as.numeric(spanL)
    
    if (shift) {
        xL = xL + minL
    }
    return (xL)
}