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layout.R 20.85 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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# plotting/layout.R
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#
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# Regroups general parameters about plotting like the theme used ang
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# color management. It mainly deals with the calling to specific
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# plotting functions and the organisation of each plot for the
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# generation of the PDF.
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# Usefull library
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library(ggplot2)
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library(scales)
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library(qpdf)
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library(gridExtra)
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library(gridtext)
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library(dplyr)
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library(grid)
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library(ggh4x)
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library(RColorBrewer)
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library(rgdal)
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library(shadowtext)
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library(png)
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# Sourcing R file
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source('plotting/datasheet.R', encoding='UTF-8')
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source('plotting/map.R', encoding='UTF-8')
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source('plotting/matrix.R', encoding='UTF-8')
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source('plotting/break.R', encoding='UTF-8')
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source('plotting/tools.R', encoding='UTF-8')
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## 1. PERSONALISATION ________________________________________________
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### 1.1. Personal theme ______________________________________________
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theme_ash =
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    theme(
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        # White background
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        panel.background=element_rect(fill='white'),
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        # Font
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        text=element_text(family='sans'),
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        # Border of plot
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        panel.border = element_rect(color="grey85",
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                                    fill=NA,
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                                    size=0.7),
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        # Grid
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        panel.grid.major.x=element_blank(),
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        panel.grid.major.y=element_blank(),
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        # Ticks marker
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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_blank(), # Axis title axis.title.x=element_blank(), axis.title.y=element_text(size=9, vjust=1.2, hjust=0.5, color='grey20'), # Axis line axis.line.x=element_blank(), axis.line.y=element_blank(), ) ### 1.2. Color palette _______________________________________________ palette_perso = c('#0f3b57', # cold '#1d7881', '#80c4a9', '#e2dac6', # mid '#fadfad', '#d08363', '#7e392f') # hot ## 2. USEFUL GENERICAL PLOT __________________________________________ ### 2.1. Void plot ___________________________________________________ # A plot completly blank void = ggplot() + geom_blank(aes(1,1)) + 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() ) ### 2.2. Contour void plot ___________________________________________ # A plot completly blank with a contour contour = void + theme(plot.background=element_rect(fill=NA, color="#EC4899"), plot.margin=margin(t=0, r=0, b=0, l=0, unit="mm")) ## 3. LAYOUT _________________________________________________________ # Generates a PDF that gather datasheets, map and summarize matrix about the trend analyses realised on selected stations layout_panel = function (df_data, df_meta, layout_matrix, what_plot=c('datasheet', 'matrix', 'map'), figdir='', filedir_opt='', filename_opt='', variable='', df_trend=NULL, alpha=0.1, unit2day=365.25, var='', type='', glose=NULL, trend_period=NULL, mean_period=NULL, colorForce=FALSE, axis_xlim=NULL, missRect=TRUE, time_header=NULL, info_header=NULL, foot_note=TRUE, info_height=2.8, time_ratio=2, var_ratio=3, foot_height=1.25, df_shapefile=NULL,
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resources_path=NULL, logo_dir=NULL, AEAGlogo_file=NULL, INRAElogo_file=NULL, FRlogo_file=NULL) { # Name of the document outfile = "Panels" # If there is an option to mention in the filename it adds it if (filename_opt != '') { outfile = paste(outfile, '_', filename_opt, sep='') } # Add the 'pdf' extensionto the name 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) } # Names of a temporary directory to store all the independent pages outdirTmp = file.path(outdir, 'tmp') # Creates it if it does not exist if (!(file.exists(outdirTmp))) { dir.create(outdirTmp) # If it already exists it deletes the pre-existent directory # and recreates one } else { unlink(outdirTmp, recursive=TRUE) dir.create(outdirTmp) } # Number of type/variable nbp = length(df_data) # Convert data tibble to list of tibble if it is not the case 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(alpha) != 'list')) { alpha = list(alpha) # If there is only one value if (length(alpha) == 1) { # Replicates the value the number of times that there # is of studied variables alpha = replicate(nbp, alpha) }} # Same if (all(class(unit2day) != 'list')) { unit2day = list(unit2day) if (length(unit2day) == 1) { unit2day = replicate(nbp, unit2day) }} if (all(class(var) != 'list')) { var = list(var) if (length(var) == 1) { var = replicate(nbp, var) }}
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if (all(class(glose) != 'list')) { glose = list(glose) if (length(glose) == 1) { glose = replicate(nbp, glose) }} 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) }} # Creates a blank list to store all the data of each type of plot list_df2plot = vector(mode='list', length=nbp) # For all the type of graph / number of studied variables for (i in 1:nbp) { # Creates a list that gather all the info for one type of graph df2plot = list(data=df_data[[i]], trend=df_trend[[i]], alpha=alpha[[i]], unit2day=unit2day[[i]], var=var[[i]], type=type[[i]], glose=glose[[i]], missRect=missRect[[i]]) # Stores it list_df2plot[[i]] = df2plot } df_page = tibble(section='Sommaire', subsection=NA, n=1) # If map needs to be plot if ('map' %in% what_plot) { df_page = map_panel(list_df2plot, df_meta, idPer_trend=length(trend_period), trend_period=trend_period, mean_period=mean_period, colorForce=colorForce, df_shapefile=df_shapefile, foot_note=foot_note, foot_height=foot_height, resources_path=resources_path, logo_dir=logo_dir, AEAGlogo_file=AEAGlogo_file, INRAElogo_file=INRAElogo_file, FRlogo_file=FRlogo_file, outdirTmp=outdirTmp, df_page=df_page) } # If summarize matrix needs to be plot if ('matrix' %in% what_plot) { df_page = matrix_panel(list_df2plot, df_meta, trend_period, mean_period, colorForce=colorForce, slice=19, outdirTmp=outdirTmp, A3=TRUE, foot_note=foot_note, foot_height=foot_height, resources_path=resources_path,
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logo_dir=logo_dir, AEAGlogo_file=AEAGlogo_file, INRAElogo_file=INRAElogo_file, FRlogo_file=FRlogo_file, df_page=df_page) } # If datasheets needs to be plot if ('datasheet' %in% what_plot) { df_page = datasheet_panel(list_df2plot, df_meta, trend_period=trend_period, mean_period=mean_period, axis_xlim=axis_xlim, colorForce=colorForce, info_header=info_header, time_header=time_header, foot_note=foot_note, layout_matrix=layout_matrix, info_height=info_height, time_ratio=time_ratio, var_ratio=var_ratio, foot_height=foot_height, resources_path=resources_path, logo_dir=logo_dir, AEAGlogo_file=AEAGlogo_file, INRAElogo_file=INRAElogo_file, FRlogo_file=FRlogo_file, outdirTmp=outdirTmp, df_page=df_page) } summary_panel(df_page, foot_note, foot_height, resources_path, logo_dir=logo_dir, AEAGlogo_file, INRAElogo_file, FRlogo_file, outdirTmp) # Combine independant pages into one PDF details = file.info(list.files(outdirTmp, full.names=TRUE)) details = details[with(details, order(as.POSIXct(mtime))),] listfile_path = rownames(details) summary_path = listfile_path[length(listfile_path)] listfile_path = listfile_path[-length(listfile_path)] listfile_path = c(summary_path, listfile_path) pdf_combine(input=listfile_path, output=file.path(outdir, outfile)) } ## 4. PDF ORGANISATION PANEL _________________________________________ ### 4.1. Summary _____________________________________________________ summary_panel = function (df_page, foot_note, foot_height, resources_path, logo_dir, AEAGlogo_file, INRAElogo_file, FRlogo_file, outdirTmp) { text_title = paste( "<b>Analyse de Stationnarité Hydrologique</b>", sep='') text_subtitle = paste( "Bassin Adour-Garonnne", sep='') Sec_name = rle(df_page$section)$values nSec = length(Sec_name)