From a8db14e8b1967781a69abef7aa49de40cb7a3f0f Mon Sep 17 00:00:00 2001
From: "louis.heraut" <louis.heraut@inrae.fr>
Date: Tue, 11 Jan 2022 19:45:37 +0100
Subject: [PATCH] Cleaned and commented
---
plotting/map.R | 9 ++-
plotting/matrix.R | 173 ++++++++++++++++++++++++++++++----------------
2 files changed, 119 insertions(+), 63 deletions(-)
diff --git a/plotting/map.R b/plotting/map.R
index 5ef6db7..d622a30 100644
--- a/plotting/map.R
+++ b/plotting/map.R
@@ -207,12 +207,17 @@ map_panel = function (list_df2plot, df_meta, df_shapefile, idPer=1, outdirTmp=''
sizerv = 0.2
}
+ # Stores the coordonate system
+ cf = coord_fixed()
+ # Makes it the default one to remove useless warning
+ cf$default = TRUE
+
# Open a new plot with the personalise theme
map = ggplot() + theme_void() +
# theme(plot.background=element_rect(fill=NA,
# color="#EC4899")) +
- # Fixed coordinate system
- coord_fixed() +
+ # Fixed coordinate system (remove useless warning)
+ cf +
# Plot the background of France
geom_polygon(data=df_france,
aes(x=long, y=lat, group=group),
diff --git a/plotting/matrix.R b/plotting/matrix.R
index fefdde0..ebf7805 100644
--- a/plotting/matrix.R
+++ b/plotting/matrix.R
@@ -162,7 +162,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
# If the p value is under the threshold
if (df_trend_code_per$p <= p_threshold){
- # Stores the mean trend
+ # Stores the averaged trend
TrendMean_code[j, i, k] = trendMean
# Otherwise
} else {
@@ -235,7 +235,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
# If the p value is under the threshold
if (df_trend_code_per$p <= p_threshold){
- # Gets the color associated to the mean trend
+ # Gets the color associated to the averaged trend
color_res = get_color(trendMean,
minTrendMean[j, i],
maxTrendMean[j, i],
@@ -269,7 +269,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
# If there is a 'mean_period'
if (!is.null(mean_period)) {
- # Blank vectors to store info about mean analyses
+ # Blank vectors to store info about breaking analysis
Periods_mean = c()
NPeriod_mean = c()
Type_mean = list()
@@ -290,7 +290,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
dataMeantmp = array(rep(NA, nbp*nCode),
dim=c(nbp, nCode))
- # For all mean period
+ # For all period of breaking analysis
for (j in 1:nPeriod_mean) {
# For all the code
for (k in 1:nCode) {
@@ -354,7 +354,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
}
}
}
- # Computes the min and the max of the mean trend for
+ # Computes the min and the max of the averaged trend for
# all the station
minBreakMean = apply(BreakMean_code, c(1, 2),
min, na.rm=TRUE)
@@ -372,7 +372,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
code = Code[k]
# For all variable
for (i in 1:nbp) {
- # Extracts break mean
+ # Extracts averaged breaking
BreakMean = BreakMean_mean[ii]
# Gets the color associated
color_res = get_color(BreakMean,
@@ -435,7 +435,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
subFill_trend = Fill_trend[CodefL_trend]
subColor_trend = Color_trend[CodefL_trend]
- # Same for mean difference analysis
+ # Same for breaking analysis
CodefL_mean = Code_mean %in% subCode
# Extracts right info
subPeriods_mean = Periods_mean[CodefL_mean]
@@ -506,12 +506,12 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
# Converts the vector of hydrological variable to
# a vector of integer associated to those variable
Xtmp = as.integer(factor(as.character(Type_trend_per)))
- # Computes X position of the column of the period dates
+ # Computes X position of the column for the period dates
Xc = j + (j - 1)*nbp*2
- # Computes X positions of columns of the mean of
+ # Computes X positions of columns for the mean of
# variables
Xm = Xtmp + (j - 1)*nbp*2 + j
- # Computes X positions of columns of the mean trend
+ # Computes X positions of columns for the averaged trend
X = Xtmp + (j - 1)*nbp*2 + nbp + j
# Computes Y positions of each line for each station
@@ -545,20 +545,20 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
# For all the variable
for (i in 1:length(X)) {
mat = mat +
- # Plots circles for mean trends
+ # Plots circles for averaged trends
gg_circle(r=0.45, xc=X[i], yc=Y[i],
fill=Fill_trend_per[i],
color=Color_trend_per[i]) +
- # Plots circles for mean of variables
+ # Plots circles for averaged of variables
gg_circle(r=0.45, xc=Xm[i], yc=Y[i],
fill='white', color='grey40') +
# Plots circles for the column of period dates
gg_circle(r=0.45, xc=Xc, yc=Y[i],
fill='white', color='grey40')
}
- # For all the mean trend on this period
+ # For all averaged trends on this periods
for (i in 1:length(TrendMean_trend_per)) {
- # Extracts the value of the mean trend
+ # Extracts the value of the averaged trend
trendMean = TrendMean_trend_per[i]
# Converts it to the right format with two
# significant figures
@@ -574,7 +574,7 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
Tcolor = 'grey85'
}
- # Same for the mean of a variable over
+ # Same for averaged variables over
# the current period
dataMean = DataMean_trend_per[i]
dataMeanC = signif(dataMean, 2)
@@ -592,8 +592,8 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
size=3, color='grey40')
}
+ # Writes a name for the period dates column
mat = mat +
- # Writes a name for the period dates column
annotate('text', x=Xc, y=max(Y) + 0.85,
label=bquote(bold('Début')),
hjust=0.5, vjust=0.5,
@@ -618,12 +618,12 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
label=bquote('[%.'*ans^{-1}*']'),
hjust=0.5, vjust=0.5,
size=2, color='grey40') +
- # Writes the type of the mean variable
+ # Writes the type of the averaged variable
annotate('text', x=Xm[i], y=max(Y) + 0.82,
label=bquote('µ'*.(type)),
hjust=0.5, vjust=0.5,
size=3.25, color='grey20') +
- # Writes the unit of the mean variable
+ # Writes the unit of the averaged variable
annotate('text', x=Xm[i], y=max(Y) + 0.6,
label=bquote('['*m^3*'.'*s^{-1}*']'),
hjust=0.5, vjust=0.5,
@@ -634,18 +634,21 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
for (k in 1:nsubCode) {
# Gets the code
code = subCode[k]
-
+ # Extracts label for the period dates
label = Periods_trend[subNPeriod_trend == j
& subCode_trend == code][1]
+ # Gets the start and end of the period
+ # for the station
periodStart = substr(label, 1, 4)
periodEnd = substr(label, 14, 17)
mat = mat +
+ # Writes the starting value
annotate('text', x=Xc, y=k + 0.13,
label=bquote(bold(.(periodStart))),
hjust=0.5, vjust=0.5,
size=3, color='grey40') +
-
+ # Writes the ending value
annotate('text', x=Xc, y=k - 0.13,
label=bquote(bold(.(periodEnd))),
hjust=0.5, vjust=0.5,
@@ -654,8 +657,10 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
}
### Mean ###
+ # For all the trend period
for (j in 1:nPeriod_mean) {
-
+ # Extracts the info to plot associated to the
+ # right period
Type_mean_per =
subType_mean[subNPeriod_mean == j]
Code_mean_per =
@@ -668,148 +673,182 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
subFill_mean[subNPeriod_mean == j]
Color_mean_per =
subColor_mean[subNPeriod_mean == j]
-
- Xtmp_mean = as.integer(factor(as.character(Type_mean_per)))
+ # Converts the vector of hydrological variable to
+ # a vector of integer associated to those variable
+ Xtmp_mean = as.integer(factor(as.character(Type_mean_per)))
+ # Computes X position of the column for the period dates
Xc_mean = j + (j - 1)*nbp + X[length(X)]
+ # Computes X positions of columns for the mean of
+ # variables
Xm_mean = Xtmp_mean + (j - 1)*nbp + j + X[length(X)]
+ # Computes X positions of columns for the difference of
+ # mean between periods (break)
Xr_mean = Xtmp_mean + (j - 1)*nbp*2 + j + X[length(X)]
-
+
+ # Computes Y positions of each line for each station
Y_mean = as.integer(factor(Code_mean_per))
+ # Position of a line to delimite periods
x = Xc_mean - 0.4
xend = Xm_mean[length(Xm_mean)] + 0.25
y = height + 1
yend = height + 1
-
+ # Drawing of the line
mat = mat +
annotate("segment",
x=x, xend=xend,
y=y, yend=yend,
color="grey40", size=0.35)
-
+
+ # Position of the name of the current period
yt = y + 0.15
Start = mean_period[[j]][1]
End = mean_period[[j]][2]
-
+ # Name of the period
periodName = bquote(bold('Période')~bold(.(as.character(j+nPeriod_trend))))
-
+ # Naming the period
mat = mat +
annotate("text", x=x, y=yt,
label=periodName,
hjust=0, vjust=0.5,
size=3, color='grey40')
-
+
+ # If this is not the first period
if (j > 1) {
+ # Position of a line to delimite results of
+ # difference of mean bewteen periods
x = Xr_mean[1] - 0.4
xend = Xr_mean[length(Xr_mean)] + 0.25
-
+ # Drawing of the line
mat = mat +
annotate("segment",
x=x, xend=xend,
y=y, yend=yend,
color="grey40", size=0.35)
-
+ # Naming the breaking columns
breakName = bquote(bold('Écart')~bold(.(as.character(j-1+nPeriod_trend)))*bold('-')*bold(.(as.character(j+nPeriod_trend))))
-
+ # Writes the name
mat = mat +
annotate("text", x=x, y=yt,
label=breakName,
hjust=0, vjust=0.5,
size=3, color='grey40')
}
-
+
+ # For all the variable
for (i in 1:length(Xm_mean)) {
mat = mat +
-
+ # Plots circles for averaged variables
gg_circle(r=0.45, xc=Xm_mean[i], yc=Y[i],
fill='white', color='grey40') +
-
+ # Plots circles for the column of period dates
gg_circle(r=0.45, xc=Xc_mean, yc=Y[i],
fill='white', color='grey40')
+ # If this is not the first period
if (j > 1) {
mat = mat +
+ # Plots circles for breaking results
gg_circle(r=0.45, xc=Xr_mean[i], yc=Y[i],
fill=Fill_mean_per[i],
color=Color_mean_per[i])
}
}
+ # For all averaged variables on this period
for (i in 1:length(DataMean_mean_per)) {
- dataMean = signif(DataMean_mean_per[i], 2)
-
+ # Extracts values of averaged variables
+ dataMean = DataMean_mean_per[i]
+ # Converts it to the right format with two
+ # significant figures
+ dataMeanC = signif(dataMean, 2)
+ # Writes averaged variables values
mat = mat +
annotate('text', x=Xm_mean[i], y=Y[i],
- label=dataMean,
+ label=dataMeanC,
hjust=0.5, vjust=0.5,
size=3, color='grey40')
-
+ # If this is not the first period
if (j > 1) {
+ # Extracts values of breaking between periods
BreakMean = BreakMean_mean_per[i]
- BreakC = signif(BreakMean*100, 2)
-
+ # Converts it to the right format with two
+ # significant figures
+ BreakMeanC = signif(BreakMean*100, 2)
+ # Writes breaking values
mat = mat +
annotate('text', x=Xr_mean[i], y=Y[i],
- label=BreakC,
+ label=BreakMeanC,
hjust=0.5, vjust=0.5,
size=3, color='white')
}
}
-
+
+ # Writes a name for the period dates column
mat = mat +
annotate('text', x=Xc_mean, y=max(Y) + 0.85,
label=bquote(bold('Début')),
hjust=0.5, vjust=0.5,
size=3, color='grey20') +
-
annotate('text', x=Xc_mean, y=max(Y) + 0.6,
label=bquote(bold('Fin')),
hjust=0.5, vjust=0.5,
size=3, color='grey20')
- # For all variable
+
+ # For all variables
for (i in 1:nbp) {
# Extract the variable of the plot
type = list_df2plot[[i]]$type
mat = mat +
+ # Writes the type of the averaged variable
annotate('text', x=Xm_mean[i], y=max(Y) + 0.82,
label=bquote('µ'*.(type)),
hjust=0.5, vjust=0.5,
size=3.25, color='grey20') +
-
+ # Writes the unit of the averaged variable
annotate('text', x=Xm_mean[i], y=max(Y) + 0.6,
label=bquote('['*m^3*'.'*s^{-1}*']'),
hjust=0.5, vjust=0.5,
size=2, color='grey40')
-
+
+ # If this is not the first period
if (j > 1) {
mat = mat +
- annotate('text', x=Xr_mean[i], y=max(Y) + 0.82,
+ # Writes the type of the breaking variable
+ annotate('text', x=Xr_mean[i],
+ y=max(Y) + 0.82,
label=bquote('d'*.(type)),
hjust=0.5, vjust=0.5,
size=3.25, color='grey20') +
-
- annotate('text', x=Xr_mean[i], y=max(Y) + 0.6,
+ # Writes the unit of the breaking variable
+ annotate('text', x=Xr_mean[i],
+ y=max(Y) + 0.6,
label=bquote('[%]'),
hjust=0.5, vjust=0.5,
size=2, color='grey40')
-
}
}
+ # For all the station on the page
for (k in 1:nsubCode) {
+ # Gets the code
code = subCode[k]
+ # Extracts label for the period dates
label = Periods_mean[subNPeriod_mean == j
& subCode_mean == code][1]
+ # Gets the start and end of the period
+ # for the station
periodStart = substr(label, 1, 4)
periodEnd = substr(label, 14, 17)
mat = mat +
+ # # Writes the starting value
annotate('text', x=Xc_mean, y=k + 0.13,
label=bquote(bold(.(periodStart))),
hjust=0.5, vjust=0.5,
size=3, color='grey40') +
-
+ # Writes the ending value
annotate('text', x=Xc_mean, y=k - 0.13,
label=bquote(bold(.(periodEnd))),
hjust=0.5, vjust=0.5,
@@ -818,21 +857,30 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
}
### Code ###
+ # For all the station
for (k in 1:nsubCode) {
# Gets the code
code = subCode[k]
+ # Gets the name of the station
name = df_meta[df_meta$code == code,]$nom
+ # Fixes a limit for the max number
+ # of characters available
ncharMax = 38
+ # If the number of character of the name is greater
+ # than the limit
if (nchar(name) > ncharMax) {
- name = paste(substr(name, 1, ncharMax), '...', sep='')
+ # Cuts the name and add '...'
+ name = paste(substr(name, 1, ncharMax),
+ '...', sep='')
}
mat = mat +
+ # Writes the code of the station
annotate('text', x=0.3, y=k + 0.14,
label=bquote(bold(.(code))),
hjust=1, vjust=0.5,
size=3.5, color="#00A3A8") +
-
+ # Writes the name of the station
annotate('text', x=0.3, y=k - 0.14,
label=name,
hjust=1, vjust=0.5,
@@ -843,31 +891,34 @@ matrix_panel = function (list_df2plot, df_meta, trend_period, mean_period, slice
mat = mat +
# Fixed coordinate system
coord_fixed() +
-
+ # X axis
scale_x_continuous(limits=c(1 - rel(6),
width + rel(0.5)),
expand=c(0, 0)) +
-
+ # Y axis
scale_y_continuous(limits=c(1 - rel(0.5),
height + rel(2)),
expand=c(0, 0))
- # Saving matrix plot
+ # Paper format in A3 if needed
if (A3) {
width = 42
height = 29.7
dpi = 300
+ # Otherwise in A4
} else {
width = 29.7
height = 21
dpi = 100
}
-
+
+ # Saving
ggsave(plot=mat,
path=outdirTmp,
- filename=paste(outnameTmp, '_', fL, imat, '.pdf',
- sep=''),
- width=width, height=height, units='cm', dpi=dpi)
+ filename=paste(outnameTmp, '_', fL,
+ imat, '.pdf', sep=''),
+ width=width, height=height,
+ units='cm', dpi=dpi)
}
}
}
--
GitLab