From 31c8c55dbd26bfb08d5343625efd6829b8740c76 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Tue, 19 Mar 2024 14:18:36 +0100
Subject: [PATCH 1/5] update image output
---
R/mod_boxplots.R | 45 +++++++++++++++++++++++++++++++++++++--------
1 file changed, 37 insertions(+), 8 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 439bd90..108a896 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -628,7 +628,8 @@ mod_boxplots_server <- function(id, r = r, session = session){
for(i in 1:length(FEAT)){
incProgress(1/length(FEAT))
tt <- stringr::str_split(FEAT[i], "__")
- ggsave(glue::glue("{tmpdir}/figures_ggplot/figures_{systim}/{sapply(tt,'[[',2)}_boxplot_{sapply(tt,'[[',1)}.{input$ImgFormat}"), listP[[FEAT[i]]], width = 20, height = 15, units = "cm", device = input$ImgFormat)
+ # ggsave(glue::glue("{tmpdir}/figures_ggplot/figures_{systim}/{sapply(tt,'[[',2)}_boxplot_{sapply(tt,'[[',1)}.{input$ImgFormat}"), listP[[FEAT[i]]], width = 20, height = 15, units = "cm", device = input$ImgFormat)
+ ggsave(glue::glue("{tmpdir}/figures_ggplot/figures_{systim}/{sapply(tt,'[[',1)}.{input$ImgFormat}"), listP[[FEAT[i]]], width = 20, height = 15, units = "cm", device = input$ImgFormat)
}
}, value = 0, message = "Generating Images...")
@@ -815,11 +816,19 @@ mod_boxplots_server <- function(id, r = r, session = session){
content <- function(file) {
print("WRITE PLOTS")
systim <- as.numeric(Sys.time())
- print(glue::glue("{tmpdir}/figures_jpgs/figures_{systim}"))
- dir.create(glue::glue("{tmpdir}/figures_jpgs/figures_{systim}"), recursive = TRUE)
+ print(glue::glue("{tmpdir}/figures_jpgs_{systim}"))
+
+ for (i in input$outtype){
+ dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}/"), recursive = TRUE)
+ }
req(r_values$tabF_melt2,r_values$fact3ok)
- tabF_melt2 <- r_values$tabF_melt2
+ tabF_melt1 <- r_values$tabF_melt2
+ save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
+ # browser()
+ tabF_melt2 <- r_values$tabF_melt2 %>%
+ separate(features, sep = "__", into = c("feat","type","unit"), remove =FALSE) %>%
+ filter(type %in% input$outtype)
print(input$ymin); print(input$ymax); print(input$steps)
@@ -870,8 +879,26 @@ mod_boxplots_server <- function(id, r = r, session = session){
met1 <- stringr::str_split_1(feat1, "__")[1] %>% stringr::str_replace("/", "_")
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)
+
+ print(input$outtype)
+ print(typ1)
+
+ print(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.jpeg"))
+
+ # print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/")) )
+
+ if(input$ImgFormat == "jpeg"){
+ jpeg(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/toto_{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
+ }else if(input$ImgFormat == "png"){
+ png(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.png"), width = 1422, height = 800, res = 150)
+ }else if(input$ImgFormat == "tiff"){
+ tiff(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.tiff"), width = 1422, height = 800, res = 150)
+ }else if(input$ImgFormat == "bmp"){
+ bmp(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.bmp"), width = 1422, height = 800, res = 150)
+ }else{
+ jpeg(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
+ }
+
# Y custom
@@ -942,8 +969,10 @@ mod_boxplots_server <- function(id, r = r, session = session){
}
# save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
-
- tar(filename, files = glue::glue("{tmpdir}/figures_jpgs/figures_{systim}") )
+ print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/area/")) )
+ print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/concentration/")) )
+ print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/ratio/")) )
+ tar(filename, files = glue::glue("{tmpdir}/figures_jpgs_{systim}/") )
file.copy(filename, file)
--
GitLab
From c273a857d26e1ab89592daa387c43accd1053a33 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 21 Mar 2024 17:23:15 +0100
Subject: [PATCH 2/5] update
---
R/mod_boxplots.R | 26 ++++++++++++++++++++++++--
1 file changed, 24 insertions(+), 2 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 108a896..6d24b75 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -888,7 +888,7 @@ mod_boxplots_server <- function(id, r = r, session = session){
# print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/")) )
if(input$ImgFormat == "jpeg"){
- jpeg(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/toto_{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
+ jpeg(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
}else if(input$ImgFormat == "png"){
png(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.png"), width = 1422, height = 800, res = 150)
}else if(input$ImgFormat == "tiff"){
@@ -969,10 +969,32 @@ mod_boxplots_server <- function(id, r = r, session = session){
}
# save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
+ print("area")
print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/area/")) )
+
+ print("conc")
print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/concentration/")) )
+
+ print("ratio")
print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/ratio/")) )
- tar(filename, files = glue::glue("{tmpdir}/figures_jpgs_{systim}/") )
+ tt <- input$outtype
+ print(tt)
+ print("TAR")
+
+ for (i in input$outtype){
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}") )
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}") )
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}") )
+ }
+
+ print("TAR2")
+ dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/output/"))
+ files <- dir(glue::glue("{tmpdir}/figures_jpgs_{systim}/"))
+ outfiles <- files[stringr::str_detect(files, ".tar")]
+
+ print(outfiles)
+
+ tar(filename, files = outfiles ) #glue::glue("{tmpdir}/figures_jpgs_{systim}/")
file.copy(filename, file)
--
GitLab
From 43e0e27a12715fc87fcc02f8d44dd338f4cb6b8e Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Fri, 22 Mar 2024 17:07:41 +0100
Subject: [PATCH 3/5] tar rbase ok
---
R/mod_boxplots.R | 67 +++++++++++++++++++++++-------------------------
1 file changed, 32 insertions(+), 35 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 6d24b75..20b1d72 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -818,14 +818,16 @@ mod_boxplots_server <- function(id, r = r, session = session){
systim <- as.numeric(Sys.time())
print(glue::glue("{tmpdir}/figures_jpgs_{systim}"))
- for (i in input$outtype){
- dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}/"), recursive = TRUE)
+ if(length(input$outtype)>1){
+ for (i in input$outtype){
+ dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}/"), recursive = TRUE)
+ }
+ }else{
+ dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/"), recursive = TRUE)
}
req(r_values$tabF_melt2,r_values$fact3ok)
tabF_melt1 <- r_values$tabF_melt2
- save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
- # browser()
tabF_melt2 <- r_values$tabF_melt2 %>%
separate(features, sep = "__", into = c("feat","type","unit"), remove =FALSE) %>%
filter(type %in% input$outtype)
@@ -880,23 +882,23 @@ mod_boxplots_server <- function(id, r = r, session = session){
met1 <- stringr::str_split_1(feat1, "__")[1] %>% stringr::str_replace("/", "_")
typ1 <- stringr::str_split_1(feat1, "__")[2] %>% stringr::str_replace("/", "_")
- print(input$outtype)
- print(typ1)
-
- print(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.jpeg"))
+ if(length(input$outtype)>1){
+ path1 <- glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/")
+ }else{
+ path1 <- glue::glue("{tmpdir}/figures_jpgs_{systim}")
+ }
- # print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/")) )
if(input$ImgFormat == "jpeg"){
- jpeg(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
+ jpeg(glue::glue("{path1}/{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
}else if(input$ImgFormat == "png"){
- png(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.png"), width = 1422, height = 800, res = 150)
+ png(glue::glue("{path1}/{met1}.png"), width = 1422, height = 800, res = 150)
}else if(input$ImgFormat == "tiff"){
- tiff(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.tiff"), width = 1422, height = 800, res = 150)
+ tiff(glue::glue("{path1}/{met1}.tiff"), width = 1422, height = 800, res = 150)
}else if(input$ImgFormat == "bmp"){
- bmp(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.bmp"), width = 1422, height = 800, res = 150)
+ bmp(glue::glue("{path1}/{met1}.bmp"), width = 1422, height = 800, res = 150)
}else{
- jpeg(glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
+ jpeg(glue::glue("{path1}/{met1}.jpeg"), width = 1422, height = 800, quality = 100, res = 150)
}
@@ -967,34 +969,29 @@ mod_boxplots_server <- function(id, r = r, session = session){
grid()
dev.off()
}
- # save(list = ls(all.names = TRUE), file = "debug.rdata", envir = environment()); print("SAVE0")
- print("area")
- print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/area/")) )
- print("conc")
- print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/concentration/")) )
+ if(length(input$outtype) > 1){
- print("ratio")
- print(dir( glue::glue("{tmpdir}/figures_jpgs_{systim}/ratio/")) )
- tt <- input$outtype
- print(tt)
- print("TAR")
+ for (i in input$outtype){
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}"))
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}"))
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}"))
+ }
- for (i in input$outtype){
- tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}") )
- tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}") )
- tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}") )
- }
+ print("TAR2")
+ # browser()
+ files <- dir(glue::glue("{tmpdir}/figures_jpgs_{systim}/"))
+ outfiles <- files[stringr::str_detect(files, ".tar")]
+
+ print(outfiles)
- print("TAR2")
- dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/output/"))
- files <- dir(glue::glue("{tmpdir}/figures_jpgs_{systim}/"))
- outfiles <- files[stringr::str_detect(files, ".tar")]
+ tar(filename, files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{outfiles}")) #glue::glue("{tmpdir}/figures_jpgs_{systim}/")
- print(outfiles)
+ }else{
+ tar(filename, files = glue::glue("{tmpdir}/figures_jpgs_{systim}/"))
+ }
- tar(filename, files = outfiles ) #glue::glue("{tmpdir}/figures_jpgs_{systim}/")
file.copy(filename, file)
--
GitLab
From 0e9ffe04601a229359241a16ceb58f4f32cdcd27 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Fri, 22 Mar 2024 17:37:27 +0100
Subject: [PATCH 4/5] tar ggplot ok
---
R/mod_boxplots.R | 45 +++++++++++++++++++++++++++++++++++++++++----
1 file changed, 41 insertions(+), 4 deletions(-)
diff --git a/R/mod_boxplots.R b/R/mod_boxplots.R
index 20b1d72..57a017a 100644
--- a/R/mod_boxplots.R
+++ b/R/mod_boxplots.R
@@ -611,7 +611,14 @@ mod_boxplots_server <- function(id, r = r, session = session){
print("WRITE PLOTS")
systim <- as.numeric(Sys.time())
print(glue::glue("{tmpdir}/figures_pngs/"))
- dir.create(glue::glue("{tmpdir}/figures_ggplot/figures_{systim}"), recursive = TRUE)
+
+ if(length(input$outtype)>1){
+ for (i in input$outtype){
+ dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}/"), recursive = TRUE)
+ }
+ }else{
+ dir.create(glue::glue("{tmpdir}/figures_jpgs_{systim}/"), recursive = TRUE)
+ }
if(input$ggstatOUT){
req(pdfall_ggstat())
@@ -627,14 +634,44 @@ mod_boxplots_server <- function(id, r = r, session = session){
withProgress({
for(i in 1:length(FEAT)){
incProgress(1/length(FEAT))
- tt <- stringr::str_split(FEAT[i], "__")
+ # tt <- stringr::str_split(FEAT[i], "__")
+ met1 <- stringr::str_split_1(FEAT[i], "__")[1] %>% stringr::str_replace("/", "_")
+ typ1 <- stringr::str_split_1(FEAT[i], "__")[2] %>% stringr::str_replace("/", "_")
+
+ if(length(input$outtype)>1){
+ path1 <- glue::glue("{tmpdir}/figures_jpgs_{systim}/{typ1}/")
+ }else{
+ path1 <- glue::glue("{tmpdir}/figures_jpgs_{systim}")
+ }
+
# ggsave(glue::glue("{tmpdir}/figures_ggplot/figures_{systim}/{sapply(tt,'[[',2)}_boxplot_{sapply(tt,'[[',1)}.{input$ImgFormat}"), listP[[FEAT[i]]], width = 20, height = 15, units = "cm", device = input$ImgFormat)
- ggsave(glue::glue("{tmpdir}/figures_ggplot/figures_{systim}/{sapply(tt,'[[',1)}.{input$ImgFormat}"), listP[[FEAT[i]]], width = 20, height = 15, units = "cm", device = input$ImgFormat)
+ ggsave(glue::glue("{path1}/{met1}.{input$ImgFormat}"), listP[[FEAT[i]]], width = 20, height = 15, units = "cm", device = input$ImgFormat)
}
}, value = 0, message = "Generating Images...")
- tar(filename, files = glue::glue("{tmpdir}/figures_ggplot/figures_{systim}") )
+ # tar(filename, files = glue::glue("{tmpdir}/figures_ggplot/figures_{systim}") )
+
+ if(length(input$outtype) > 1){
+
+ for (i in input$outtype){
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}"))
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}"))
+ tar(glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}.tar"), files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{i}"))
+ }
+
+ print("TAR2")
+ # browser()
+ files <- dir(glue::glue("{tmpdir}/figures_jpgs_{systim}/"))
+ outfiles <- files[stringr::str_detect(files, ".tar")]
+
+ print(outfiles)
+
+ tar(filename, files = glue::glue("{tmpdir}/figures_jpgs_{systim}/{outfiles}")) #glue::glue("{tmpdir}/figures_jpgs_{systim}/")
+
+ }else{
+ tar(filename, files = glue::glue("{tmpdir}/figures_jpgs_{systim}/"))
+ }
file.copy(filename, file)
--
GitLab
From 95c41e68d63c2500c12a99a29c107e1c4c93c352 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Mon, 25 Mar 2024 10:24:15 +0100
Subject: [PATCH 5/5] fix xlab
---
DESCRIPTION | 2 +-
R/app_ui.R | 2 +-
R/mod_plots_isot.R | 8 ++++----
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index ae5ea6d..4a6b2bb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: graphstatsr
Title: graphstatsr
-Version: 2.0.0
+Version: 2.1.0
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
diff --git a/R/app_ui.R b/R/app_ui.R
index 81e2599..644d2f9 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 2.0.0",
+ title = "GraphStatsR 2.1.0",
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")),
diff --git a/R/mod_plots_isot.R b/R/mod_plots_isot.R
index 816f63a..9bbd9a7 100644
--- a/R/mod_plots_isot.R
+++ b/R/mod_plots_isot.R
@@ -278,7 +278,7 @@ mod_plots_isot_server <- function(id, r = r, session = session){
p3_bar <- p3_bar_group <- ggplot(tabhisto2, aes(x = get(input$group1), y = MeanGroupEnrC13)) +
geom_bar(stat="identity", color="black", fill = "#b6bced",
position=position_dodge()) +
- theme_bw() + ylab("Mean EnrC13") +
+ theme_bw() + ylab("Mean EnrC13") + xlab(input$group1) +
theme(legend.position = "None",
axis.text.x = element_text(
angle = 45, hjust=1)) +
@@ -289,7 +289,7 @@ mod_plots_isot_server <- function(id, r = r, session = session){
p4_bar <- p4_bar_group <- ggplot(tabhisto2, aes(x = get(input$group1), y = MeanGroupArea)) +
geom_bar(stat="identity", color="black", fill = "#b6bced",
position=position_dodge()) +
- theme_bw() + ylab("Mean TotalArea") +
+ theme_bw() + ylab("Mean TotalArea") + xlab(input$group1) +
theme(legend.position = "None",
axis.text.x = element_text(
angle = 45, hjust=1)) +
@@ -602,7 +602,7 @@ mod_plots_isot_server <- function(id, r = r, session = session){
LL[[glue::glue("{i}_enrC13")]] <- p3_bar_group <- ggplot(tabhisto2, aes(x = get(input$group1), y = MeanGroupEnrC13)) +
geom_bar(stat="identity", color="black", fill = "#b6bced",
position=position_dodge()) +
- theme_bw() + ylab("Mean EnrC13") +
+ theme_bw() + ylab("Mean EnrC13") + xlab("") +
theme(legend.position = "None",
axis.text.x = element_text(
angle = 45, hjust=1)) +
@@ -613,7 +613,7 @@ mod_plots_isot_server <- function(id, r = r, session = session){
LL[[glue::glue("{i}_area")]] <- p4_bar_group <- ggplot(tabhisto2, aes(x = get(input$group1), y = MeanGroupArea)) +
geom_bar(stat="identity", color="black", fill = "#b6bced",
position=position_dodge()) +
- theme_bw() + ylab("Mean TotalArea") +
+ theme_bw() + ylab("Mean TotalArea") + xlab("") +
theme(legend.position = "None",
axis.text.x = element_text(
angle = 45, hjust=1)) +
--
GitLab