|
|
@ -9,6 +9,9 @@ library(openCyto) |
|
|
|
library(flowCore) |
|
|
|
library(flowWorkspace) |
|
|
|
library(CytoML) |
|
|
|
library(ggcyto) |
|
|
|
|
|
|
|
filter<-dplyr::filter |
|
|
|
|
|
|
|
print(getwd()) |
|
|
|
source("../sqlFunctions.R", encoding = "UTF-8") |
|
|
@ -73,7 +76,8 @@ ui <- fluidPage( |
|
|
|
mainPanel( |
|
|
|
htmlOutput("report"), |
|
|
|
h3("Nitrogen"), |
|
|
|
tableOutput("nitrogen") |
|
|
|
tableOutput("nitrogen"), |
|
|
|
plotOutput("visorplot") |
|
|
|
) |
|
|
|
), |
|
|
|
|
|
|
@ -83,13 +87,20 @@ ui <- fluidPage( |
|
|
|
selectInput("phenotype", "Tipo de análisis", selected="Pop", choices=c("Pop", "IC")), |
|
|
|
), |
|
|
|
mainPanel( |
|
|
|
actionButton("goButtonDir","Selecciona directorio fenotipo"), |
|
|
|
textOutput("session"), |
|
|
|
hr(), |
|
|
|
actionButton("fcsconvert", "Convertir a fcs"), |
|
|
|
hr(), |
|
|
|
actionButton("pngexport", "Exportar informes"), |
|
|
|
actionButton("popexport", "Actualizar BBDD") |
|
|
|
tabsetPanel( |
|
|
|
tabPanel("Entrada", |
|
|
|
actionButton("goButtonDir","Selecciona directorio fenotipo"), |
|
|
|
textOutput("session"), |
|
|
|
hr(), |
|
|
|
actionButton("fcsconvert", "Convertir a fcs"), |
|
|
|
hr(), |
|
|
|
actionButton("pngexport", "Exportar informes"), |
|
|
|
actionButton("popexport", "Actualizar BBDD") |
|
|
|
), |
|
|
|
tabPanel("Visor", |
|
|
|
|
|
|
|
) |
|
|
|
) |
|
|
|
) |
|
|
|
), |
|
|
|
|
|
|
@ -843,50 +854,128 @@ server <- function(input, output) { |
|
|
|
}) |
|
|
|
|
|
|
|
observeEvent(input$pngexport,{ |
|
|
|
route<-cito_dir |
|
|
|
|
|
|
|
ws<-open_flowjo_xml(paste0(route,"Populations.wsp")) |
|
|
|
gs<-flowjo_to_gatingset(ws, name="All Samples") |
|
|
|
|
|
|
|
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% |
|
|
|
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
|
|
|
|
|
|
|
for (samp in sampleNames(gs)){ |
|
|
|
print(samp) |
|
|
|
p<-autoplot(gs[[samp]], bins=64) |
|
|
|
ggsave(paste0(route, samp,".png"),p,width = 10, height = 10) |
|
|
|
if (input$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$phenotype == "IC"){ |
|
|
|
route<-cito_dir |
|
|
|
|
|
|
|
ws<-open_flowjo_xml(paste0(route,"IC.wsp")) |
|
|
|
gs<-flowjo_to_gatingset(ws, name="All Samples") |
|
|
|
|
|
|
|
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% |
|
|
|
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
|
|
|
|
|
|
|
names<-sampleNames(gs) %>% gsub("ab|Ab|AB|iso|Iso|ISO| ","",.) %>% unique() |
|
|
|
|
|
|
|
nodes<-gs_get_pop_paths(gs) |
|
|
|
nodes_parent<-nodes[!grepl("CTLA4|LAG3|PD1|TIGIT|TIM3|root$", nodes)] |
|
|
|
nodes_cd4<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD4/",nodes)] |
|
|
|
nodes_cd8<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD8/",nodes)] |
|
|
|
|
|
|
|
for (id in names){ |
|
|
|
print(id) |
|
|
|
iso<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("iso",sampleNames(gs))] |
|
|
|
ab<-sampleNames(gs)[grepl(id, sampleNames(gs)) & grepl("ab",sampleNames(gs))] |
|
|
|
|
|
|
|
g1<-ggcyto_arrange(autoplot(gs[[ab]], nodes_parent, bins=128), nrow=1) |
|
|
|
g2<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd8, bins=64), nrow=1) |
|
|
|
g3<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd8, bins=64), nrow=1) |
|
|
|
g4<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd4, bins=64), nrow=1) |
|
|
|
g5<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd4, bins=64), nrow=1) |
|
|
|
g_all<-gridExtra::gtable_rbind(g1,g2,g3,g4,g5) |
|
|
|
ggsave(paste0(route,id,".IC.png"), g_all, width = 10, height = 10) |
|
|
|
} |
|
|
|
} |
|
|
|
}) |
|
|
|
|
|
|
|
observeEvent(input$popexport,{ |
|
|
|
route<-cito_dir |
|
|
|
|
|
|
|
ws<-open_flowjo_xml(paste0(route,"Populations.wsp")) |
|
|
|
gs<-flowjo_to_gatingset(ws, name="All Samples") |
|
|
|
|
|
|
|
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "Pop ")[[1]][2]) %>% |
|
|
|
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
|
|
|
|
|
|
|
nodes<-sapply(strsplit(gs_get_pop_paths(gs), "/"), tail, 1) |
|
|
|
nodes<-nodes[grepl("_",nodes)] |
|
|
|
pop<-gs_pop_get_stats(gs, nodes=nodes,type="percent") %>% as.data.frame %>% mutate(percent=percent*100) |
|
|
|
|
|
|
|
pop[,"pop"]<-gsub("_","",pop$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) |
|
|
|
|
|
|
|
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.") |
|
|
|
|
|
|
|
}) |
|
|
|
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$percent, digits=2) |
|
|
|
pop_sp<-pop %>% spread(pop, percent) |
|
|
|
|
|
|
|
vartypes<-rep("Number", pop_sp %>% select(-samples) %>% colnames %>% length) |
|
|
|
names(vartypes)<-pop_sp %>% select(-samples) %>% colnames |
|
|
|
|
|
|
|
sqlSave(dta, pop_sp, tablename="POPULATIONS", append = T, varTypes = vartypes, rownames = F) |
|
|
|
print("Tabla POPULATIONS sincronizada.") |
|
|
|
} |
|
|
|
if (input$phenotype == "IC"){ |
|
|
|
route<-cito_dir |
|
|
|
|
|
|
|
ws<-open_flowjo_xml(paste0(route,"IC.wsp")) |
|
|
|
gs<-flowjo_to_gatingset(ws, name="All Samples") |
|
|
|
|
|
|
|
sampleNames(gs)<-sapply(sampleNames(gs), function(x) strsplit(x, "ICs ")[[1]][2]) %>% |
|
|
|
gsub("[[:space:]][0-9]*.fcs_.[0-9]*","", . , perl = T) |
|
|
|
|
|
|
|
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$|LAG3$|TIGIT$|/CTLA4â\u0081»$|/TIM3â\u0081»$|/PD1â\u0081»$|/LAG3â\u0081»$|/TIGITâ\u0081»$", 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$pop<-gsub(" ", "_", pop$pop) |
|
|
|
|
|
|
|
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) |
|
|
|
pop_sp <- rename(pop_sp, "samples"="sample") |
|
|
|
|
|
|
|
vartypes<-rep("Number", pop_sp %>% select(-samples, -Population) %>% colnames %>% length) |
|
|
|
names(vartypes)<-pop_sp %>% select(-samples, -Population) %>% colnames |
|
|
|
|
|
|
|
sqlSave(dta, pop_sp, tablename="IC", append = T, varTypes = vartypes, rownames = F) |
|
|
|
print("Tabla IC sincronizada.") |
|
|
|
} |
|
|
|
}) |
|
|
|
|
|
|
|
|
|
|
|
## scRNAseq ---- |
|
|
|
|
|
|
|