marcelcosta/BDAccess
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Completado procesado de datos de Checkpoint Inhibitors.

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marcelcosta
2022-04-04 17:14:42 +02:00
parent 67ba4921ca
commit ab1684651e
1 changed files with 137 additions and 48 deletions
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BDAccess/app.R
+137 -48
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@@ -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.")
})
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 ----