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Heraut Louis authoredd15e12b3
# \\\# 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 librarylibrary(ggplot2)library(scales)library(qpdf)library(gridExtra)library(gridtext)library(dplyr)library(grid)library(ggh4x)library(RColorBrewer)library(rgdal)library(shadowtext)# Sourcing R filesource('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 themetheme_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'),7172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140
# 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)
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}}
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)
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}
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)
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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)
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} 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)
}