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+435 -0CitoProcess/app.R
| @ -0,0 +1,435 @@ | |||||
| library(shiny) | |||||
| library(openCyto) | |||||
| library(flowCore) | |||||
| library(flowWorkspace) | |||||
| library(CytoML) | |||||
| library(ggcyto) | |||||
| # library(reshape2) | |||||
| # library(CitFuns) | |||||
| library(openxlsx) | |||||
| library(tidyverse) | |||||
| # Define UI for application that draws a histogram | |||||
| ui <- fluidPage( | |||||
| # Application title | |||||
| titlePanel("Análisis Citometría ImmunoPreserve"), | |||||
| # Sidebar with a slider input for number of bins | |||||
| sidebarLayout( | |||||
| sidebarPanel( | |||||
| selectInput("phenotype", "Panel", selected="Panel1", choices=c("Panel1", "Panel2","Panel3","panel4")), | |||||
| ), | |||||
| mainPanel( | |||||
| textInput("cytopath", label="Directorio fenotipo", value=""), | |||||
| actionButton("goButtonDir","Selecciona directorio fenotipo"), | |||||
| textOutput("session"), | |||||
| hr(), | |||||
| actionButton("fcsconvert", "Convertir a fcs"), | |||||
| hr(), | |||||
| actionButton("pngexport", "Exportar informes"), | |||||
| hr(), | |||||
| textInput("dbpath", label="Ruta Base de Dades", value=""), | |||||
| actionButton("goButtondbpath","Selecciona Ruta Base de Dades"), | |||||
| textOutput("sessiondbpath"), | |||||
| actionButton("popexport", "Actualizar BBDD") | |||||
| ) | |||||
| ) | |||||
| ) | |||||
| # Define server logic required to draw a histogram | |||||
| server <- function(input, output) { | |||||
| observe({ | |||||
| if(input$goButtonDir > 0){ | |||||
| if (input$cytopath == ""){ | |||||
| cito_dir<<-choose.dir() %>% gsub("\\","/",. ,fixed=T) %>% paste0("/") %>% stringi::stri_enc_tonative() | |||||
| }else{ | |||||
| cito_dir<<-input$cytopath %>% gsub("\\","/",. ,fixed=T) %>% gsub("/$", "", .) %>% paste0("/") %>% stringi::stri_enc_tonative() | |||||
| } | |||||
| output$session <- renderText( | |||||
| cito_dir | |||||
| ) | |||||
| } | |||||
| }) | |||||
| observe({ | |||||
| if(input$goButtondbpath > 0){ | |||||
| if (input$dbpath == ""){ | |||||
| db_path<<-choose.dir() %>% gsub("\\","/",. ,fixed=T) %>% paste0("/") %>% stringi::stri_enc_tonative() | |||||
| }else{ | |||||
| db_path<<-input$dbpath %>% gsub("\\","/",. ,fixed=T) %>% gsub("/$", "", .) %>% paste0("/") %>% stringi::stri_enc_tonative() | |||||
| } | |||||
| output$sessiondbpath <- renderText( | |||||
| db_path | |||||
| ) | |||||
| } | |||||
| }) | |||||
| observeEvent(input$fcsconvert,{ | |||||
| route<-cito_dir | |||||
| files<-list.files(route, ".LMD") | |||||
| for (lmd in files){ | |||||
| fcs<-read.FCS(paste0(route,lmd), dataset = 2) | |||||
| keyword(fcs)['$FIL']<-paste0(gsub(".LMD","",lmd), ".fcs") | |||||
| write.FCS(fcs, paste0(route, gsub(".LMD","",lmd), ".fcs")) | |||||
| } | |||||
| print("Conversión completada") | |||||
| }) | |||||
| observeEvent(input$pngexport,{ | |||||
| # if (input$phenotype == "Pop"){ | |||||
| # route<-cito_dir | |||||
| # | |||||
| # ws<-open_flowjo_xml(paste0(route,"Populations.wsp")) | |||||
| # gs<-flowjo_to_gatingset(ws, name="All Samples") | |||||
| # | |||||
| # sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% | |||||
| # gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) | |||||
| # | |||||
| # for (samp in sampleNames(gs)){ | |||||
| # print(samp) | |||||
| # p<-autoplot(gs[[samp]], bins=64) | |||||
| # ggsave(paste0(route, samp,".pop.png"),p,width = 10, height = 10) | |||||
| # } | |||||
| # } | |||||
| if (input$phenotype == "Panel1"){ | |||||
| route<-cito_dir | |||||
| ws<-open_flowjo_xml(paste0(route,"Panel1.wsp")) | |||||
| gs<-flowjo_to_gatingset(ws, name="All Samples") | |||||
| sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Panel1 ")[[1]][2]) %>% | |||||
| gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) | |||||
| gs<-gs[sampleNames(gs)[!grepl("Iso|ISO|iso",sampleNames(gs))]] | |||||
| bool.comb<-apply( | |||||
| expand.grid(c("","!"), c("","!"), c("","!"), c("","!")), | |||||
| 1, | |||||
| function(x) paste0(x[1],"CTLA4 & ",x[2],"LAG3 & ",x[3],"PD1 & ",x[4], "TIM3") | |||||
| ) | |||||
| bool.name<-apply( | |||||
| expand.grid(c("+","-"), c("+","-"), c("+","-"), c("+","-")), | |||||
| 1, | |||||
| function(x) paste0("CTLA4",x[1]," LAG3",x[2]," PD1",x[3]," TIM3",x[4]) | |||||
| ) | |||||
| print("Booleanos CD8") | |||||
| for (i in 1:length(bool.comb)){ | |||||
| call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i]))) | |||||
| boolgate<-eval(call) | |||||
| gs_pop_add(gs, boolgate, parent="_CD8", name = bool.name[i]) | |||||
| } | |||||
| print("Booleanos CD4") | |||||
| for (i in 1:length(bool.comb)){ | |||||
| call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i]))) | |||||
| boolgate<-eval(call) | |||||
| gs_pop_add(gs, boolgate, parent="_CD4", name = bool.name[i]) | |||||
| } | |||||
| recompute(gs) | |||||
| names<-sampleNames(gs) # %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique() | |||||
| nodes<-gs_get_pop_paths(gs) | |||||
| # nodes<-gsub("â\u0081»", "-", nodes) | |||||
| # nodes<-gsub("â\u0081º", "+", nodes) | |||||
| nodes<-nodes[grepl("CTLA4", nodes)] | |||||
| nodes<-nodes[!grepl("_CD4$|_CD8$|CTLA4$|TIM3$|PD1$|LAG3$", nodes)] | |||||
| pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) | |||||
| pop$percent<-round(pop$percent, digits=2) | |||||
| # pop$pop<-gsub("â\u0081»", "n", pop$pop) | |||||
| # pop$pop<-gsub("â\u0081º", "p", pop$pop) | |||||
| pop$pop<-gsub("-", "n", pop$pop, fixed=T) | |||||
| pop$pop<-gsub("+", "p", pop$pop, fixed=T) | |||||
| pop$pop<-gsub(" ", "_", pop$pop) | |||||
| ## Esto si no hay isotipo | |||||
| pop_sp<-pop | |||||
| pop_sp["Population"]<-str_extract(pop_sp$pop, "/_CD[4,8]{1}/") %>% gsub("/|_","",.) | |||||
| pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1) | |||||
| pop_sp<-pop_sp %>% spread(pop, percent) | |||||
| ## Esto si hay Isotipo | |||||
| # pop["Type"]<-"ab" | |||||
| # pop[grepl("iso|ISO|Iso",pop$sample),"Type"]<-"iso" | |||||
| # pop$sample<-gsub("iso|ISO|Iso|ab|AB|Ab| ","",pop$sample) | |||||
| # pop_sp<-pop %>% spread(Type, percent) | |||||
| # pop_sp["Net"]<-pop_sp$ab | |||||
| # pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"Net"]<-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"ab"]-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"iso"] | |||||
| # pop_sp$Net[pop_sp$Net < 0]<-0 | |||||
| # pop_sp["Population"]<-str_extract(pop_sp$pop, "/CD[4,8]{1}/") %>% gsub("/","",.) | |||||
| # pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1) | |||||
| # | |||||
| # pop_sp<-pop_sp %>% select(-ab,-iso) %>% spread(pop,Net) | |||||
| # pop_sp$CTLA4n_LAG3n_PD1n_TIGITn_TIM3n<- pop_sp %>% select(-CTLA4n_LAG3n_PD1n_TIGITn_TIM3n) %>% group_by(sample,Population) %>% | |||||
| # gather(pop, value, -sample,-Population) %>% summarise(n=100-sum(value)) %>% pull(n) | |||||
| # if (input$dbtype == "OV"){ | |||||
| # pop_sp <- rename(pop_sp, "samples"="sample") | |||||
| # } | |||||
| # if (input$dbtype %in% c("UM", "CC")){ | |||||
| # pop_sp <- rename(pop_sp, "CODIGO"="sample") | |||||
| # | |||||
| pop_sql<-read.xlsx(paste0(db_path,"Panel1.xlsx"), sheet = "IC") | |||||
| pop_sp<-pop_sp %>% merge(pop_sql %>% slice(0), all=T) %>% select(colnames(pop_sql)) | |||||
| for (id in names){ | |||||
| print(id) | |||||
| # iso<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("iso|Iso|ISO",sampleNames(gs))] | |||||
| # ab<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("ab|Ab|AB",sampleNames(gs))] | |||||
| data<-pop_sp %>% filter(sample == id) | |||||
| data1<-data %>% gather(phen, value, -sample, -Population) | |||||
| data1$phen<-gsub("p","+",data1$phen) | |||||
| data1$phen<-gsub("n","-",data1$phen) | |||||
| data1$phen<-gsub("_"," ",data1$phen) | |||||
| data1$phen<-gsub("n","-",data1$phen, fixed = T) | |||||
| data1$phen<-gsub("p","+",data1$phen, fixed = T) | |||||
| data1$phen<-gsub("_"," ",data1$phen) | |||||
| data1[data1$value < 1, "phen"]<-"Other" | |||||
| data1$phen<-gsub("[A-Z]*-*[0-9T]- *", "", data1$phen) | |||||
| data1$phen<-gsub("+ $", "", data1$phen) | |||||
| data1$phen[data1$phen == ""]<-"All Negative" | |||||
| data1["phen1"]<-"PD1" | |||||
| data1[!grepl("PD1+", data1$phen),"phen1"]<-NA | |||||
| data1["phen2"]<-"TIM3" | |||||
| data1[!grepl("TIM3+", data1$phen),"phen2"]<-NA | |||||
| data1["phen3"]<-"CTLA4" | |||||
| data1[!grepl("CTLA4+", data1$phen),"phen3"]<-NA | |||||
| data1["phen4"]<-"LAG3" | |||||
| data1[!grepl("LAG3+", data1$phen),"phen4"]<-NA | |||||
| data1<-data1 %>% arrange(desc(value)) | |||||
| data2<-data1 %>% filter(!phen %in% c("All Negative","Other")) | |||||
| data1<-rbind(data2, data1 %>% filter(phen %in% c("All Negative","Other")) %>% arrange(desc(phen))) | |||||
| data_cd8<-data1 %>% filter(Population == "CD8") | |||||
| data_cd4<-data1 %>% filter(Population == "CD4") | |||||
| data_cd8$ymax<-cumsum(data_cd8$value) | |||||
| data_cd8$ymin<-c(0, head(data_cd8$ymax, n=-1)) | |||||
| data_cd4$ymax<-cumsum(data_cd4$value) | |||||
| data_cd4$ymin<-c(0, head(data_cd4$ymax, n=-1)) | |||||
| data1<-rbind(data_cd8, data_cd4) | |||||
| color<-c(c("CTLA4+ LAG3+ PD1+ TIM3+"="black","All Negative"="grey90","Other"="grey50", "PD1+"="#C07AFF", "CTLA4+"="#3EB3DE","TIM3+"="#5EF551","LAG3+"="#DEBB3E"), | |||||
| c("CTLA4+ PD1+"="#6666FF","PD1+ TIM3+"="#849CA8", "LAG3+ PD1+"="#C47F9F", "CTLA4+ TIM3+"="#4ED498", "CTLA4+ LAG3+"="#8EB78E", "LAG3+ TIM3+"="#9ED848"), | |||||
| c("CTLA4+ PD1+ TIM3+"="#B81515", "LAG3+ PD1+ TIM3+"="#0f5860")) | |||||
| basic.color<-color[c("PD1+","TIM3+","CTLA4+","LAG3+")] | |||||
| names(basic.color)<-c("PD1","TIM3","CTLA4","LAG3") | |||||
| # Make the plot | |||||
| g_coex<-ggplot(data1)+ | |||||
| facet_grid(.~factor(Population, levels=c("CD8","CD4")))+ | |||||
| geom_rect(aes(ymax=ymax, ymin=ymin, xmax=4.5, xmin=0), fill=color[data1$phen])+ | |||||
| geom_rect(aes(ymax=ymax, ymin=ymin, xmax=5.4, xmin=5, fill=factor(phen1, levels=c("PD1","TIM3","CTLA4","LAG3"))))+ | |||||
| geom_rect(aes(ymax=ymax, ymin=ymin, xmax=5.9, xmin=5.5, fill=factor(phen2, levels=c("PD1","TIM3","CTLA4","LAG3"))))+ | |||||
| geom_rect(aes(ymax=ymax, ymin=ymin, xmax=6.4, xmin=6, fill=factor(phen3, levels=c("PD1","TIM3","CTLA4","LAG3"))))+ | |||||
| geom_rect(aes(ymax=ymax, ymin=ymin, xmax=6.9, xmin=6.5, fill=factor(phen4, levels=c("PD1","TIM3","CTLA4","LAG3"))))+ | |||||
| scale_fill_manual(values = basic.color, na.value="#FFFFFF00", drop=F, limits=c("PD1","TIM3","CTLA4","LAG3"), name="IC")+ | |||||
| coord_polar(theta="y") + # Try to remove that to understand how the chart is built initially | |||||
| xlim(c(0, 8)) +# Try to remove that to see how to make a pie chart | |||||
| theme_classic()+ | |||||
| theme(strip.background = element_blank(), | |||||
| strip.text = element_text(size=12, face="bold"), | |||||
| axis.line = element_blank(), | |||||
| axis.ticks = element_blank(), | |||||
| # plot.margin = margin(-200,0,0,0), | |||||
| axis.text = element_blank()) | |||||
| nodes<-gs_get_pop_paths(gs) | |||||
| nodes_parent<-nodes[!grepl("CTLA4|LAG3|PD1|TIM3|root$", nodes)] | |||||
| nodes_cd4<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIM3$", nodes) & grepl("/_CD4/",nodes)] | |||||
| nodes_cd8<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIM3$", nodes) & grepl("/_CD8/",nodes)] | |||||
| g1<-ggcyto_arrange(autoplot(gs[[id]], nodes_parent), nrow=2) | |||||
| g2<-ggcyto_arrange(autoplot(gs[[id]], nodes_cd8), nrow=1) | |||||
| g3<-ggcyto_arrange(autoplot(gs[[id]], nodes_cd4), nrow=1) | |||||
| g_dots<-gridExtra::gtable_rbind(g1,g2,g3) | |||||
| g_all<-ggpubr::ggarrange(g_dots, g_coex, ncol=1, heights=c(0.75,0.25)) | |||||
| ggsave(paste0(route,id,".IC.png"), g_all, width = 10, height = 14) | |||||
| ggsave(paste0(db_path, "Informes/",id,".IC.png"), g_all, width = 10, height = 14) | |||||
| } | |||||
| print("Informes finalizados!") | |||||
| } | |||||
| }) | |||||
| observeEvent(input$popexport,{ | |||||
| if (input$phenotype == "Pop"){ | |||||
| route<-cito_dir | |||||
| ws<-open_flowjo_xml(paste0(route,"Populations.wsp")) | |||||
| gs<-flowjo_to_gatingset(ws, name="All Samples") | |||||
| sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% | |||||
| gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) | |||||
| nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1) | |||||
| nodes<-nodes[grepl("_",nodes)] | |||||
| pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) | |||||
| pop[,"pop"]<-gsub("_","",pop$pop) | |||||
| pop$pop<-gsub(" ","_",pop$pop) | |||||
| pop$pop<-gsub("+","pos",pop$pop, fixed=T) | |||||
| pop$pop<-gsub("-","neg",pop$pop, fixed=T) | |||||
| pop<-rename(pop, "samples"="sample") | |||||
| pop$percent<-round(pop$percent, digits=2) | |||||
| pop_sp<-pop %>% spread(pop, percent) | |||||
| pop_sql<-sqlFetch(dta, "POPULATIONS") %>% slice(0) | |||||
| pop_sp<-pop_sp %>% merge(pop_sql, all=T) %>% select(colnames(pop_sql)) | |||||
| vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length) | |||||
| names(vartypes)<-pop_sp %>% select(-samples) %>% colnames | |||||
| sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F) | |||||
| print("Tabla POPULATIONS sincronizada.") | |||||
| } | |||||
| if (input$phenotype == "Panel1"){ | |||||
| route<-cito_dir | |||||
| ws<-open_flowjo_xml(paste0(route,"Panel1.wsp")) | |||||
| gs<-flowjo_to_gatingset(ws, name="All Samples") | |||||
| sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Panel1 ")[[1]][2]) %>% | |||||
| gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) | |||||
| gs<-gs[sampleNames(gs)[!grepl("Iso|ISO|iso",sampleNames(gs))]] | |||||
| bool.comb<-apply( | |||||
| expand.grid(c("","!"), c("","!"), c("","!"), c("","!")), | |||||
| 1, | |||||
| function(x) paste0(x[1],"CTLA4 & ",x[2],"LAG3 & ",x[3],"PD1 & ",x[4], "TIM3") | |||||
| ) | |||||
| bool.name<-apply( | |||||
| expand.grid(c("+","-"), c("+","-"), c("+","-"), c("+","-")), | |||||
| 1, | |||||
| function(x) paste0("CTLA4",x[1]," LAG3",x[2]," PD1",x[3]," TIM3",x[4]) | |||||
| ) | |||||
| print("Booleanos CD8") | |||||
| for (i in 1:length(bool.comb)){ | |||||
| call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i]))) | |||||
| boolgate<-eval(call) | |||||
| gs_pop_add(gs, boolgate, parent="_CD8", name = bool.name[i]) | |||||
| } | |||||
| print("Booleanos CD4") | |||||
| for (i in 1:length(bool.comb)){ | |||||
| call<-substitute(booleanFilter(v), list(v=as.symbol(bool.comb[i]))) | |||||
| boolgate<-eval(call) | |||||
| gs_pop_add(gs, boolgate, parent="_CD4", name = bool.name[i]) | |||||
| } | |||||
| recompute(gs) | |||||
| names<-sampleNames(gs) # %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique() | |||||
| nodes<-gs_get_pop_paths(gs) | |||||
| # nodes<-gsub("â\u0081»", "-", nodes) | |||||
| # nodes<-gsub("â\u0081º", "+", nodes) | |||||
| nodes<-nodes[grepl("CTLA4", nodes)] | |||||
| nodes<-nodes[!grepl("_CD4$|_CD8$|CTLA4$|TIM3$|PD1$|LAG3$", nodes)] | |||||
| pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) | |||||
| pop$percent<-round(pop$percent, digits=2) | |||||
| # pop$pop<-gsub("â\u0081»", "n", pop$pop) | |||||
| # pop$pop<-gsub("â\u0081º", "p", pop$pop) | |||||
| pop$pop<-gsub("-", "n", pop$pop, fixed=T) | |||||
| pop$pop<-gsub("+", "p", pop$pop, fixed=T) | |||||
| pop$pop<-gsub(" ", "_", pop$pop) | |||||
| ## Esto si no hay isotipo | |||||
| pop_sp<-pop | |||||
| pop_sp["Population"]<-str_extract(pop_sp$pop, "/_CD[4,8]{1}/") %>% gsub("/|_","",.) | |||||
| pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1) | |||||
| pop_sp<-pop_sp %>% spread(pop, percent) | |||||
| ## Esto si hay Isotipo | |||||
| # pop["Type"]<-"ab" | |||||
| # pop[grepl("iso|ISO|Iso",pop$sample),"Type"]<-"iso" | |||||
| # pop$sample<-gsub("iso|ISO|Iso|ab|AB|Ab| ","",pop$sample) | |||||
| # pop_sp<-pop %>% spread(Type, percent) | |||||
| # pop_sp["Net"]<-pop_sp$ab | |||||
| # pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"Net"]<-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"ab"]-pop_sp[!grepl("CTLA4n_LAG3n_PD1n_TIGITn_TIM3n",pop_sp$pop),"iso"] | |||||
| # pop_sp$Net[pop_sp$Net < 0]<-0 | |||||
| # pop_sp["Population"]<-str_extract(pop_sp$pop, "/CD[4,8]{1}/") %>% gsub("/","",.) | |||||
| # pop_sp$pop<-sapply(strsplit(pop_sp$pop, "/"), tail, 1) | |||||
| # | |||||
| # pop_sp<-pop_sp %>% select(-ab,-iso) %>% spread(pop,Net) | |||||
| # pop_sp$CTLA4n_LAG3n_PD1n_TIGITn_TIM3n<- pop_sp %>% select(-CTLA4n_LAG3n_PD1n_TIGITn_TIM3n) %>% group_by(sample,Population) %>% | |||||
| # gather(pop, value, -sample,-Population) %>% summarise(n=100-sum(value)) %>% pull(n) | |||||
| # if (input$dbtype == "OV"){ | |||||
| # pop_sp <- rename(pop_sp, "samples"="sample") | |||||
| # } | |||||
| # if (input$dbtype %in% c("UM", "CC")){ | |||||
| # pop_sp <- rename(pop_sp, "CODIGO"="sample") | |||||
| # | |||||
| pop_sql<-read.xlsx(paste0(db_path,"Panel1.xlsx"), sheet = "IC") | |||||
| pop_sp<-pop_sp %>% merge(pop_sql %>% slice(0), all=T) %>% select(colnames(pop_sql)) | |||||
| ic_sp<-rbind(pop_sql, pop_sp) | |||||
| nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1) | |||||
| nodes<-gs_get_pop_paths(gs)[grepl("_",nodes)] | |||||
| pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) | |||||
| pop<-pop %>% mutate(Population=str_extract(pop, "/_CD[4,8]{1}/"), | |||||
| Population=case_when(is.na(Population)~"", | |||||
| Population == "/_CD4/"~"_CD4", | |||||
| Population == "/_CD8/"~"_CD8", | |||||
| TRUE~Population), | |||||
| pop=gsub("_","",pop), | |||||
| pop=paste0(pop,Population)) %>% select(-Population) | |||||
| pop$pop<-sapply(strsplit(pop$pop, "/"), tail, 1) | |||||
| pop$pop<-gsub(" ","_",pop$pop) | |||||
| # pop$pop<-gsub("+","pos",pop$pop, fixed=T) | |||||
| # pop$pop<-gsub("-","neg",pop$pop, fixed=T) | |||||
| # pop<-rename(pop, "samples"="sample") | |||||
| pop$percent<-round(pop$percent, digits=2) | |||||
| pop_sp<-pop %>% spread(pop, percent) | |||||
| pop_sql<-read.xlsx(paste0(db_path,"Panel1.xlsx"), sheet = "POPULATIONS") | |||||
| pop_sp<-pop_sp %>% merge(pop_sql %>% slice(0), all=T) %>% select(colnames(pop_sql)) | |||||
| pop_sp<-rbind(pop_sql,pop_sp) | |||||
| write.xlsx(list("IC"=ic_sp, "POPULATIONS"=pop_sp), paste0(db_path, "Panel1.xlsx")) | |||||
| print("Tabla Panel1 sincronizada.") | |||||
| } | |||||
| }) | |||||
| } | |||||
| # Run the application | |||||
| shinyApp(ui = ui, server = server) | |||||