From 0ef9c448fc7b51ccb605deb7849b8d19fd8e4967 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 29 Feb 2024 11:22:54 +0100
Subject: [PATCH 1/8] add yaxis custom settings
---
R/mod_boxplots.R | 21 +++++++++++++--------
1 file changed, 13 insertions(+), 8 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 78d6a9b..8c19dc9 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -64,7 +64,10 @@ mod_boxplots_ui <- function(id){
materialSwitch(ns("ggplotstats1"), label = "Display ggstatsplot", value = TRUE, status = "primary"),
materialSwitch(ns("plotall"), label = "Plot all conditions (even NAs)", value = TRUE, status = "primary"),
materialSwitch(ns("grey_mode"), label = "Colored boxplot", value = TRUE, status = "primary"),
- materialSwitch(ns("y0"), label = "Set y lower limit to 0", value = TRUE, status = "primary"),
+ materialSwitch(ns("ySci"), label = "Yaxis scientific numbers:", value = TRUE, status = "primary"),
+ numericInput(ns("ymin"), "Y min:", 0),
+ numericInput(ns("ymax"), "Y max:", NA),
+ numericInput(ns("ysteps"), "Y steps:", NA),
width = 6
),
column(
@@ -294,8 +297,13 @@ mod_boxplots_server <- function(id, r = r, session = session){
labs(fill="")')
eval(parse(text=fun))
- if(input$y0){
- p <- p + coord_cartesian(ylim = c(0, NA ))
+
+ if(is.na(input$ysteps)){
+ # Y custom
+ p <- p + coord_cartesian(ylim = c(input$ymin, input$ymax)) + scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
+ }else{
+ p <- p + scale_y_continuous(breaks = seq(input$ymin, input$ymax, input$ysteps),
+ labels = function(x) format(x, scientific = input$ySci))
}
if(!input$grey_mode){
@@ -320,14 +328,11 @@ mod_boxplots_server <- function(id, r = r, session = session){
fun <- glue::glue('
ggstats <- ggbetweenstats(tabfeat, {r_values$fact3ok}, value, type = "nonparametric",
p.adjust.method = "fdr", pairwise.display = "significant", xlab = "", ylab = ytitle,
- outlier.tagging = TRUE, outlier.label = "sample.id", results.subtitle = FALSE, title = input$feat1)
+ outlier.tagging = TRUE, outlier.label = "sample.id", results.subtitle = FALSE, title = input$feat1) +
+ coord_cartesian(ylim = c(0, NA))
')
eval(parse(text=fun))
- if(input$y0){
- ggstats <- ggstats + coord_cartesian(ylim = c(0, NA))
- }
-
r_values$ggstats <- ggstats
outlist$ggstats <- ggstats
}
--
GitLab
From 693bc45a1e44f8e2d491902b2f57c89455d3e3ad Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 29 Feb 2024 12:05:03 +0100
Subject: [PATCH 2/8] update
---
R/mod_boxplots.R | 26 +++++++++++++++-----------
1 file changed, 15 insertions(+), 11 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 8c19dc9..78df188 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -298,14 +298,16 @@ mod_boxplots_server <- function(id, r = r, session = session){
eval(parse(text=fun))
- if(is.na(input$ysteps)){
# Y custom
- p <- p + coord_cartesian(ylim = c(input$ymin, input$ymax)) + scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
- }else{
+ p <- p + coord_cartesian(ylim = c(input$ymin, input$ymax)) +
+ scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
+
+ if(!is.na(input$ysteps)){
p <- p + scale_y_continuous(breaks = seq(input$ymin, input$ymax, input$ysteps),
labels = function(x) format(x, scientific = input$ySci))
}
+
if(!input$grey_mode){
p <- p +
geom_boxplot(fill = "grey")
@@ -450,9 +452,14 @@ mod_boxplots_server <- function(id, r = r, session = session){
labs(fill="")')
eval(parse(text=fun))
- if(input$y0){
- listP[[FEAT[i]]] <- listP[[FEAT[i]]] + coord_cartesian(ylim = c(0, NA ))
- }
+ # Y custom
+ listP[[FEAT[i]]] <- listP[[FEAT[i]]] + coord_cartesian(ylim = c(input$ymin, input$ymax)) +
+ scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
+
+ if(!is.na(input$ysteps)){
+ listP[[FEAT[i]]] <- listP[[FEAT[i]]] + scale_y_continuous(breaks = seq(input$ymin, input$ymax, input$ysteps),
+ labels = function(x) format(x, scientific = input$ySci))
+ }
if(input$outlier_labs){
listP[[FEAT[i]]] <- listP[[FEAT[i]]] +
@@ -550,14 +557,11 @@ mod_boxplots_server <- function(id, r = r, session = session){
fun <- glue::glue('
listP[[FEAT[i]]] <- ggbetweenstats(tabfeat, {r_values$fact3ok}, value, type = "nonparametric",
p.adjust.method = "fdr", pairwise.display = "significant", xlab = "", ylab = ytitle,
- outlier.tagging = TRUE, outlier.label = "sample.id", title = FEAT[i], results.subtitle = FALSE)')
+ outlier.tagging = TRUE, outlier.label = "sample.id", title = FEAT[i], results.subtitle = FALSE) +
+ coord_cartesian(ylim = c(0, NA))')
eval(parse(text=fun))
- if(input$y0){
- listP[[FEAT[i]]] <- listP[[FEAT[i]]] + coord_cartesian(ylim = c(0, NA))
- }
-
# print("WRITE PLOTS")
# dir.create(paste(tmpdir, "/figures_ggstat/", sep = ""), recursive = TRUE)
# print(paste(tmpdir, "/figures_ggstat/", sep = ""))
--
GitLab
From 29dbf60e4710bfb0b52aaede492e7abee7b6e278 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 29 Feb 2024 15:07:00 +0100
Subject: [PATCH 3/8] yaxis ggplot ok
---
R/mod_boxplots.R | 44 +++++++++++++++++++++++++++++++++-----------
1 file changed, 33 insertions(+), 11 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 78df188..edbea03 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -60,10 +60,11 @@ mod_boxplots_ui <- function(id){
column(
h3("General settings"),
- textInput(ns("custom_ytitle"), "Custom y title", "None"),
materialSwitch(ns("ggplotstats1"), label = "Display ggstatsplot", value = TRUE, status = "primary"),
materialSwitch(ns("plotall"), label = "Plot all conditions (even NAs)", value = TRUE, status = "primary"),
materialSwitch(ns("grey_mode"), label = "Colored boxplot", value = TRUE, status = "primary"),
+ h3("Y axis settings"),
+ textInput(ns("custom_ytitle"), "Custom y title", "None"),
materialSwitch(ns("ySci"), label = "Yaxis scientific numbers:", value = TRUE, status = "primary"),
numericInput(ns("ymin"), "Y min:", 0),
numericInput(ns("ymax"), "Y max:", NA),
@@ -182,11 +183,14 @@ mod_boxplots_server <- function(id, r = r, session = session){
)
)
+ updateNumericInput(session, "ymax", label = glue::glue("Ymax: (max value in dataset: {format(max(r_values$subsetds_final_melt$value, na.rm = TRUE), scientific = TRUE, digits = 2)})"),
+ value = NA )
+
}
})
- boxtab <- eventReactive(c(input$go4, input$go3), { #
+ boxtab <- reactive({
cat(file=stderr(), 'BOXTAB', "\n")
req(r_values$subsetds_final_melt, input$fact3, r$ds1())
r_values$tabF_melt2 <- tabF_melt2 <- tabF_melt <- r_values$subsetds_final_melt
@@ -302,11 +306,19 @@ mod_boxplots_server <- function(id, r = r, session = session){
p <- p + coord_cartesian(ylim = c(input$ymin, input$ymax)) +
scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
- if(!is.na(input$ysteps)){
+ if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
+ print("ycustom1")
p <- p + scale_y_continuous(breaks = seq(input$ymin, input$ymax, input$ysteps),
labels = function(x) format(x, scientific = input$ySci))
}
+ if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
+ print("ycustom2")
+ p <- p + coord_cartesian(ylim = c(0, max(tabfeat$value, na.rm = TRUE))) +
+ scale_y_continuous(breaks = seq(0, max(tabfeat$value, na.rm = TRUE), input$ysteps),
+ labels = function(x) format(x, scientific = input$ySci))
+ }
+
if(!input$grey_mode){
p <- p +
@@ -452,14 +464,24 @@ mod_boxplots_server <- function(id, r = r, session = session){
labs(fill="")')
eval(parse(text=fun))
- # Y custom
- listP[[FEAT[i]]] <- listP[[FEAT[i]]] + coord_cartesian(ylim = c(input$ymin, input$ymax)) +
- scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
-
- if(!is.na(input$ysteps)){
- listP[[FEAT[i]]] <- listP[[FEAT[i]]] + scale_y_continuous(breaks = seq(input$ymin, input$ymax, input$ysteps),
- labels = function(x) format(x, scientific = input$ySci))
- }
+ # Y custom
+ listP[[FEAT[i]]] <- listP[[FEAT[i]]] + coord_cartesian(ylim = c(input$ymin, input$ymax)) +
+ scale_y_continuous(labels = function(x) format(x, scientific = input$ySci))
+
+ if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
+ print("ycustom1")
+ listP[[FEAT[i]]] <- listP[[FEAT[i]]] + scale_y_continuous(breaks = seq(input$ymin, input$ymax, input$ysteps),
+ labels = function(x) format(x, scientific = input$ySci))
+ }
+
+ if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
+ print("ycustom2")
+ listP[[FEAT[i]]] <- listP[[FEAT[i]]] + coord_cartesian(ylim = c(0, max(tabfeat$value, na.rm = TRUE))) +
+ scale_y_continuous(breaks = seq(0, max(tabfeat$value, na.rm = TRUE), input$ysteps),
+ labels = function(x) format(x, scientific = input$ySci))
+ }
+
+
if(input$outlier_labs){
listP[[FEAT[i]]] <- listP[[FEAT[i]]] +
--
GitLab
From 6b8f2a89eddddaed9decf35c1066920f03473925 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 29 Feb 2024 16:41:13 +0100
Subject: [PATCH 4/8] update
---
R/mod_boxplots.R | 25 +++++++++++++++++++++++--
1 file changed, 23 insertions(+), 2 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index edbea03..e3a7ff1 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -827,16 +827,37 @@ mod_boxplots_server <- function(id, r = r, session = session){
typ1 <- stringr::str_split_1(feat1, "__")[2] %>% stringr::str_replace("/", "_")
jpeg(glue::glue("{tmpdir}/figures_jpgs/figures_{systim}/{typ1}_boxplot_{met1}.jpeg"),
width = 1422, height = 800, quality = 100, res = 150)
+
+ # Y custom
+
+ if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
+ print("ycustom1")
+ YLIM <- c(input$ymin, input$ymax)
+ STEPS <- seq(input$ymin, input$ymax, input$steps)
+ }
+
+ if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
+ print("ycustom2")
+ YLIM <- c(0, max(tab1$value, na.rm = TRUE))
+ STEPS <- seq(0, max(tab1$value, na.rm = TRUE), input$steps)
+ }
+ fact3 <- r_values$fact3ok
+ save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
if(input$outlier_labs){
car::Boxplot(as.formula(glue::glue("value~{r_values$fact3ok}")), data = tab1, main = feat1,
cex.main = 0.6, boxwex=.3, col = gg_color_hue(nrow(unique(tab1[r_values$fact3ok]))),
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = YLAB,
- ylim=c(0,max(tab1$value, na.rm = TRUE)))
+ ylim=YLIM, axes = FALSE)
+ axis(1); axis(2, at = STEPS)
+ #c(0,max(tab1$value, na.rm = TRUE))
+
}else{
boxplot(as.formula(glue::glue("value~{r_values$fact3ok}")), data = tab1, main = feat1,
cex.main = 0.6, boxwex=.3, col = gg_color_hue(nrow(unique(tab1[r_values$fact3ok]))),
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = "area",
- ylim=c(0,max(tab1$value, na.rm = TRUE)))
+ ylim=YLIM, axes = FALSE)
+ axis(1); axis(2, at = STEPS)
+ #c(0,max(tab1$value, na.rm = TRUE))
}
grid()
--
GitLab
From d9b9b66bdeae4e5fe908ffee9f98c1cd51914bc2 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Fri, 1 Mar 2024 17:33:33 +0100
Subject: [PATCH 5/8] update
---
R/mod_boxplots.R | 19 ++++++++++++++-----
1 file changed, 14 insertions(+), 5 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index e3a7ff1..c8a9421 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -829,26 +829,33 @@ mod_boxplots_server <- function(id, r = r, session = session){
width = 1422, height = 800, quality = 100, res = 150)
# Y custom
+
+ if(!is.na(input$ymin) & is.na(input$ysteps) & is.na(input$ymax) ){
+ YLIM <- c(0, max(tab1$value, na.rm = TRUE))
+ STEPS <- NULL
+ }
if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
print("ycustom1")
YLIM <- c(input$ymin, input$ymax)
- STEPS <- seq(input$ymin, input$ymax, input$steps)
+ STEPS <- format(seq(input$ymin, input$ymax, input$steps), scientific = input$ySci)
}
if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
print("ycustom2")
YLIM <- c(0, max(tab1$value, na.rm = TRUE))
- STEPS <- seq(0, max(tab1$value, na.rm = TRUE), input$steps)
+ STEPS <- format(seq(0, max(tab1$value, na.rm = TRUE), input$steps), scientific = input$ySci)
}
+
fact3 <- r_values$fact3ok
- save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
+
if(input$outlier_labs){
car::Boxplot(as.formula(glue::glue("value~{r_values$fact3ok}")), data = tab1, main = feat1,
cex.main = 0.6, boxwex=.3, col = gg_color_hue(nrow(unique(tab1[r_values$fact3ok]))),
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = YLAB,
ylim=YLIM, axes = FALSE)
- axis(1); axis(2, at = STEPS)
+ axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
+ axis(2, at = STEPS, cex.axis = 0.6); graphics::box()
#c(0,max(tab1$value, na.rm = TRUE))
}else{
@@ -856,13 +863,15 @@ mod_boxplots_server <- function(id, r = r, session = session){
cex.main = 0.6, boxwex=.3, col = gg_color_hue(nrow(unique(tab1[r_values$fact3ok]))),
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = "area",
ylim=YLIM, axes = FALSE)
- axis(1); axis(2, at = STEPS)
+ axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
+ axis(2, at = STEPS, cex.axis = 0.6); graphics::box()
#c(0,max(tab1$value, na.rm = TRUE))
}
grid()
dev.off()
}
+ save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
tar(filename, files = glue::glue("{tmpdir}/figures_jpgs/figures_{systim}") )
--
GitLab
From d4a3c9e54b806723a5ff7bfe0fb40b600a427cc8 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Mon, 4 Mar 2024 17:36:07 +0100
Subject: [PATCH 6/8] update
---
R/mod_boxplots.R | 30 +++++++++++++++++++++++++-----
1 file changed, 25 insertions(+), 5 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index c8a9421..940bf14 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -777,7 +777,8 @@ mod_boxplots_server <- function(id, r = r, session = session){
req(r_values$tabF_melt2,r_values$fact3ok)
tabF_melt2 <- r_values$tabF_melt2
-
+ print(input$ymin); print(input$ymax); print(input$steps)
+
for(i in 1:length(levels(tabF_melt2$features))){
if(input$nbPicPage == 4){
@@ -830,15 +831,26 @@ mod_boxplots_server <- function(id, r = r, session = session){
# Y custom
+ #validate steps
+
+
if(!is.na(input$ymin) & is.na(input$ysteps) & is.na(input$ymax) ){
+ print("ycustom01")
YLIM <- c(0, max(tab1$value, na.rm = TRUE))
STEPS <- NULL
}
+
+ if(!is.na(input$ymin) & is.na(input$ysteps) & !is.na(input$ymax) ){
+ print("ycustom02")
+ YLIM <- c(0, input$ymax)
+ STEPS <- NULL
+ }
if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
print("ycustom1")
+ print(input$ymin); print(input$ymax); print(input$ysteps)
YLIM <- c(input$ymin, input$ymax)
- STEPS <- format(seq(input$ymin, input$ymax, input$steps), scientific = input$ySci)
+ STEPS <- format(seq(input$ymin, input$ymax, input$ysteps), scientific = input$ySci)
}
if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
@@ -847,6 +859,14 @@ mod_boxplots_server <- function(id, r = r, session = session){
STEPS <- format(seq(0, max(tab1$value, na.rm = TRUE), input$steps), scientific = input$ySci)
}
+ # HERE
+ # if(!is.na(input$steps) & length(STEPS)> 100){
+ # print("Too much steps on Y axis.")
+ # print(length(STEPS))
+ # validate("Too much steps on Y axis.")
+ # return()
+ # }
+
fact3 <- r_values$fact3ok
if(input$outlier_labs){
@@ -855,7 +875,7 @@ mod_boxplots_server <- function(id, r = r, session = session){
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = YLAB,
ylim=YLIM, axes = FALSE)
axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
- axis(2, at = STEPS, cex.axis = 0.6); graphics::box()
+ axis(2, at = STEPS, cex.axis = 0.6, labels=format(STEPS,scientific=input$ySci)); graphics::box()
#c(0,max(tab1$value, na.rm = TRUE))
}else{
@@ -864,14 +884,14 @@ mod_boxplots_server <- function(id, r = r, session = session){
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = "area",
ylim=YLIM, axes = FALSE)
axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
- axis(2, at = STEPS, cex.axis = 0.6); graphics::box()
+ axis(2, at = STEPS, cex.axis = 0.6, labels=format(STEPS,scientific=input$ySci)); graphics::box()
#c(0,max(tab1$value, na.rm = TRUE))
}
grid()
dev.off()
}
- save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
+ # save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
tar(filename, files = glue::glue("{tmpdir}/figures_jpgs/figures_{systim}") )
--
GitLab
From a089de20347fe19d964001c9e250421eadb19450 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Fri, 15 Mar 2024 09:57:24 +0100
Subject: [PATCH 7/8] update
---
R/mod_boxplots.R | 74 +++++++++++++++++++++++++++++++++++++++---------
1 file changed, 61 insertions(+), 13 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 940bf14..a9454bf 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -747,22 +747,65 @@ mod_boxplots_server <- function(id, r = r, session = session){
next
}
+
+ # Y custom
+
+ #validate steps
+ if(!is.na(input$ymin) & is.na(input$ysteps) & is.na(input$ymax) ){
+ # print("ycustom01")
+ YLIM <- c(0, max(tab1$value, na.rm = TRUE))
+ STEPS <- NULL
+ }
+
+ if(!is.na(input$ymin) & is.na(input$ysteps) & !is.na(input$ymax) ){
+ # print("ycustom02")
+ YLIM <- c(input$ymin, input$ymax)
+ STEPS <- NULL
+ }
+
+ if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
+ # print("ycustom1")
+ print(input$ymin); print(input$ymax); print(input$ysteps)
+ YLIM <- c(input$ymin, input$ymax)
+ STEPS <- format(seq(input$ymin, input$ymax, input$ysteps), scientific = input$ySci)
+ }
+
+ if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
+ # print("ycustom2")
+ YLIM <- c(0, max(tab1$value, na.rm = TRUE))
+ STEPS <- format(seq(0, max(tab1$value, na.rm = TRUE), input$steps), scientific = input$ySci)
+ }
+
+ fact3 <- r_values$fact3ok
+
if(input$outlier_labs){
car::Boxplot(as.formula(glue::glue("value~{r_values$fact3ok}")), data = tab1, main = feat1,
cex.main = 0.6, boxwex=.3, col = gg_color_hue(nrow(unique(tab1[r_values$fact3ok]))),
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = YLAB,
- ylim=c(0,max(tab1$value, na.rm = TRUE)))
+ ylim=YLIM, axes = FALSE)
+ axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
+ if(!is.null(STEPS)){
+ axis(2, at = STEPS, cex.axis = 0.6, labels=format(as.numeric(STEPS), scientific=TRUE)); graphics::box()
+ }else{
+ axis(2); graphics::box()
+ }
+
}else{
boxplot(as.formula(glue::glue("value~{r_values$fact3ok}")), data = tab1, main = feat1,
cex.main = 0.6, boxwex=.3, col = gg_color_hue(nrow(unique(tab1[r_values$fact3ok]))),
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = "area",
- ylim=c(0,max(tab1$value, na.rm = TRUE)))
+ ylim=YLIM, axes = FALSE)
+ axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
+ if(!is.null(STEPS)){
+ axis(2, at = STEPS, cex.axis = 0.6, labels=format(as.numeric(STEPS), scientific=TRUE)); graphics::box()
+ }else{
+ axis(2); graphics::box()
+ }
}
grid()
}
dev.off()
-
})
output$downloadTAR_rbase <- downloadHandler(
@@ -832,29 +875,27 @@ mod_boxplots_server <- function(id, r = r, session = session){
# Y custom
#validate steps
-
-
if(!is.na(input$ymin) & is.na(input$ysteps) & is.na(input$ymax) ){
- print("ycustom01")
+ # print("ycustom01")
YLIM <- c(0, max(tab1$value, na.rm = TRUE))
STEPS <- NULL
}
if(!is.na(input$ymin) & is.na(input$ysteps) & !is.na(input$ymax) ){
- print("ycustom02")
- YLIM <- c(0, input$ymax)
+ # print("ycustom02")
+ YLIM <- c(input$ymin, input$ymax)
STEPS <- NULL
}
if(!is.na(input$ysteps) & !is.na(input$ymin) & !is.na(input$ymax) ){
- print("ycustom1")
+ # print("ycustom1")
print(input$ymin); print(input$ymax); print(input$ysteps)
YLIM <- c(input$ymin, input$ymax)
STEPS <- format(seq(input$ymin, input$ymax, input$ysteps), scientific = input$ySci)
}
if( is.na(input$ymin) | is.na(input$ymax) & !is.na(input$ysteps) ){
- print("ycustom2")
+ # print("ycustom2")
YLIM <- c(0, max(tab1$value, na.rm = TRUE))
STEPS <- format(seq(0, max(tab1$value, na.rm = TRUE), input$steps), scientific = input$ySci)
}
@@ -875,7 +916,11 @@ mod_boxplots_server <- function(id, r = r, session = session){
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = YLAB,
ylim=YLIM, axes = FALSE)
axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
- axis(2, at = STEPS, cex.axis = 0.6, labels=format(STEPS,scientific=input$ySci)); graphics::box()
+ if(!is.null(STEPS)){
+ axis(2, at = STEPS, cex.axis = 0.6, labels=format(STEPS,scientific=input$ySci)); graphics::box()
+ }else{
+ axis(2); graphics::box()
+ }
#c(0,max(tab1$value, na.rm = TRUE))
}else{
@@ -884,8 +929,11 @@ mod_boxplots_server <- function(id, r = r, session = session){
cex.lab = 0.9, cex.axis = 0.5, las = 2, xlab = "", ylab = "area",
ylim=YLIM, axes = FALSE)
axis(1, at= 1:length(levels(tab1[,r_values$fact3ok])), labels = levels(tab1[,r_values$fact3ok]), las = 2, cex.axis = 0.6)
- axis(2, at = STEPS, cex.axis = 0.6, labels=format(STEPS,scientific=input$ySci)); graphics::box()
- #c(0,max(tab1$value, na.rm = TRUE))
+ if(!is.null(STEPS)){
+ axis(2, at = STEPS, cex.axis = 0.6, labels=format(STEPS,scientific=input$ySci)); graphics::box()
+ }else{
+ axis(2); graphics::box()
+ }
}
grid()
--
GitLab
From d8f8ab6c998598ab4ca85c0492860d7a495e1e91 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Fri, 15 Mar 2024 10:05:48 +0100
Subject: [PATCH 8/8] document version
---
DESCRIPTION | 6 +++---
R/app_ui.R | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 234e9b4..d2a8b25 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: graphstatsr
Title: graphstatsr
-Version: 1.9.1
+Version: 1.10.0
Authors@R:
person("Etienne", "Rifa", , "etienne.rifa@insa-toulouse.fr", role = c("cre", "aut"))
Description: A shiny app to easily generate advanced graphics and some non
@@ -20,11 +20,11 @@ Imports:
ggstatsplot,
glue,
golem (>= 0.3.1),
+ graphics,
gridExtra,
htmltools,
plotly,
PMCMRplus,
- RColorBrewer,
reshape2,
rhdf5,
shiny (>= 1.6.0),
@@ -47,4 +47,4 @@ Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/R/app_ui.R b/R/app_ui.R
index e122d07..2e4b70a 100644
--- a/R/app_ui.R
+++ b/R/app_ui.R
@@ -19,7 +19,7 @@ app_ui <- function(request) {
# )
dashboardPage(skin = "red",
dashboardHeader(
- title = "GraphStatsR 1.9.1",
+ title = "GraphStatsR 1.10.0",
tags$li(class="dropdown",tags$a("Hosted by", img(src = SK8img,
title = "SK8", height = "20px"), headerText = "Source code",href="https://sk8.inrae.fr/", target="_blank")),
--
GitLab