diff --git a/server.R b/server.R
index d457e5a..6cbe87f 100644
--- a/server.R
+++ b/server.R
@@ -79,16 +79,16 @@ server <- function(input, output) {
return(res)
}
- getIndex <- function() {
+ scmapCluster_index <- function() {
if (input$data_type == "existing") {
# load indexes
- files <- list.files(paste0("www/refs/", input$organism), pattern = ".csv")
+ files <- list.files(paste0("www/scmap-cluster/", input$organism), pattern = ".csv")
index <- list()
for (f in files) {
name <- strsplit(f, "\\.")[[1]][1]
tmp <- read.csv(
paste0(
- "www/refs/",
+ "www/scmap-cluster/",
input$organism, "/", f
)
)
@@ -114,29 +114,74 @@ server <- function(input, output) {
return(index)
}
+ scmapCell_index <- function() {
+ if (input$data_type == "existing") {
+ # load indexes
+ files <- list.files(paste0("www/scmap-cell/", input$organism), pattern = ".rds")
+ index <- list()
+ for (f in files) {
+ name <- strsplit(f, "\\.")[[1]][1]
+ tmp <- readRDS(
+ paste0(
+ "www/scmap-cell/",
+ input$organism, "/", f
+ )
+ )
+ index[[name]] <- tmp
+ }
+ } else {
+ # compute the index
+ dataset <- values$reference_data()
+ if(values$features) {
+ rowData(dataset)$scmap_features <- values$scmap_features
+ rowData(dataset)$scmap_scores <- values$scmap_scores
+ } else {
+ dataset <- selectFeatures(dataset)
+ }
+ index <- indexCell(
+ dataset
+ )
+ index <- list(metadata(index)$scmap_cell_index)
+ }
+ return(index)
+ }
+
scmap <- function() {
- # compute index
- index <- getIndex()
-
# run scmap-cluster
+ index_cluster <- scmapCluster_index()
scmapCluster_results <- scmapCluster(
values$projection_data(),
- index_list = index
+ index_list = index_cluster
)
if(!"SingleCellExperiment" %in% is(scmapCluster_results)) {
# summarise results of scmap-cluster
- values$scmap_cluster_siml <- scmapCluster_results$scmap_cluster_siml
- values$scmap_cluster_labs <- scmapCluster_results$scmap_cluster_labs
- values$scmap_cluster_comb <- scmapCluster_results$combined_labs
+ values$scmap_cluster_res <- scmapCluster_results
values$scmap_cluster_all <-
- scmapClusterResults2table(index, scmapCluster_results$scmap_cluster_labs)
+ scmapClusterResults2table(index_cluster, scmapCluster_results$scmap_cluster_labs)
values$scmap_cluster_combined <-
- scmapClusterResults2table(index, data.frame(scmapCluster_results$combined_labs))
+ scmapClusterResults2table(index_cluster, data.frame(scmapCluster_results$combined_labs))
} else {
values$scmap_cluster_worked <- FALSE
}
+
+ if(input$run_scmap_cell == "Yes") {
+ # run scmap-cell
+ index_cell <- scmapCell_index()
+ scmapCell_results <- scmapCell(
+ values$projection_data(),
+ index_list = index_cell
+ )
+ if("list" %in% is(scmapCell_results)) {
+ # summarise results of scmap-cell
+ values$scmap_cell_all <- scmapCell_results
+ } else {
+ print(class(scmapCell_results))
+ values$scmap_cell_worked <- FALSE
+ }
+ }
+
return()
}
@@ -205,35 +250,50 @@ server <- function(input, output) {
)
})
- output$results_cluster <- renderUI({
+ output$results <- renderUI({
switch(input$data_type,
"own" = list(
+ fluidRow(
box(width = 12,
- title = "Results",
+ title = "scmap-cluster",
DT::dataTableOutput('results_table'),
- downloadButton("scmap_cluster_labs", 'Download All Assignments'),
- downloadButton("scmap_cluster_siml", 'Download All Similarities'),
+ downloadButton("scmap_cluster_all", 'Download'),
solidHeader = TRUE,
status = "success"
+ ),
+ conditionalPanel("input.run_scmap_cell == 'Yes'",
+ box(width = 12,
+ title = "scmap-cell",
+ downloadButton("scmap_cell_all", 'Download'),
+ solidHeader = TRUE,
+ status = "success"
+ )
)
+ )
),
"existing" = list(
fluidRow(
box(width = 12,
- title = "Individual Results",
+ title = "scmap-cluster",
DT::dataTableOutput('results_table'),
- downloadButton("scmap_cluster_labs", 'Download All Assignments'),
- downloadButton("scmap_cluster_siml", 'Download All Similarities'),
+ downloadButton("scmap_cluster_all", 'Download'),
solidHeader = TRUE,
status = "success"
),
box(width = 12,
- title = "Consensus Results",
+ title = "scmap-cluster (combined)",
DT::dataTableOutput('consensus_results_table'),
- downloadButton("consensus_results_assignments", 'Download Consensus Assignments'),
solidHeader = TRUE,
status = "success"
- )
+ ),
+ conditionalPanel("input.run_scmap_cell == 'Yes'",
+ box(width = 12,
+ title = "scmap-cell",
+ downloadButton("scmap_cell_all", 'Download'),
+ solidHeader = TRUE,
+ status = "success"
+ )
+ )
)
)
)
@@ -331,30 +391,21 @@ server <- function(input, output) {
values$feature_table <- row_data
})
- output$scmap_cluster_labs <- downloadHandler(
+ output$scmap_cluster_all <- downloadHandler(
filename = function() {
- paste('scmap_results_assignments.csv', sep='')
+ 'scmap-cluster.rds'
},
content = function(con) {
- write.csv(values$scmap_cluster_labs, con, quote = FALSE)
+ saveRDS(values$scmap_cluster_res, con)
}
)
- output$scmap_cluster_siml <- downloadHandler(
+ output$scmap_cell_all <- downloadHandler(
filename = function() {
- paste('scmap_results_similarities.csv', sep='')
+ 'scmap-cell.rds'
},
content = function(con) {
- write.csv(values$scmap_cluster_siml, con, quote = FALSE)
- }
- )
-
- output$consensus_results_assignments <- downloadHandler(
- filename = function() {
- paste('scmap_results_consensus.csv', sep='')
- },
- content = function(con) {
- write.csv(values$scmap_cluster_comb, con, quote = FALSE)
+ saveRDS(values$scmap_cell_all, con)
}
)
@@ -367,10 +418,12 @@ server <- function(input, output) {
})
output$reference_data <- reactive({
values$scmap_cluster_worked <- TRUE
+ values$scmap_cell_worked <- TRUE
return(!is.null(values$reference_data()))
})
output$projection_data <- reactive({
values$scmap_cluster_worked <- TRUE
+ values$scmap_cell_worked <- TRUE
return(!is.null(values$projection_data()))
})
output$reference_feature_symbol <- reactive({
@@ -404,6 +457,10 @@ server <- function(input, output) {
return(values$scmap_cluster_worked)
})
+ output$scmap_cell_worked <- reactive({
+ return(values$scmap_cell_worked)
+ })
+
# make output variables visible for the client side
outputOptions(output, "projection_file", suspendWhenHidden = FALSE)
outputOptions(output, "reference_file", suspendWhenHidden = FALSE)
@@ -414,4 +471,5 @@ server <- function(input, output) {
outputOptions(output, "pdata_cell_types", suspendWhenHidden = FALSE)
outputOptions(output, "features", suspendWhenHidden = FALSE)
outputOptions(output, "scmap_cluster_worked", suspendWhenHidden = FALSE)
+ outputOptions(output, "scmap_cell_worked", suspendWhenHidden = FALSE)
}
diff --git a/ui.R b/ui.R
index eb60c7c..8237fe7 100644
--- a/ui.R
+++ b/ui.R
@@ -25,7 +25,7 @@ dashboardPage(
menuItem("About", tabName = "about", icon = icon("bank")),
menuItem("Datasets", tabName = "datasets", icon = icon("cloud-upload")),
menuItem("Features", tabName = "features", icon = icon("gears")),
- menuItem("scmap-cluster", tabName = "results_cluster", icon = icon("area-chart"))
+ menuItem("Results", tabName = "results", icon = icon("area-chart"))
)
)
),
@@ -40,7 +40,7 @@ dashboardPage(
sidebarMenu(
menuItem("About", tabName = "about", icon = icon("bank")),
menuItem("Datasets", tabName = "datasets", icon = icon("cloud-upload")),
- menuItem("scmap-cluster", tabName = "results_cluster", icon = icon("area-chart"))
+ menuItem("Results", tabName = "results", icon = icon("area-chart"))
)
)
)
@@ -155,6 +155,14 @@ dashboardPage(
solidHeader = TRUE
)
),
+ box(width = 12,
+ HTML("Would you like to run scmap-cell? (may take some time)
"),
+ radioButtons("run_scmap_cell", NULL,
+ c("No" = "No",
+ "Yes" = "Yes"),
+ selected = "No"),
+ solidHeader = TRUE
+ ),
solidHeader = TRUE,
status = "primary"
)
@@ -206,39 +214,20 @@ dashboardPage(
)
)
),
- tabItem(tabName = "results_cluster",
+ tabItem(tabName = "results",
fluidRow(
- conditionalPanel("input.data_type == 'own'",
- box(width = 12,
- title = "Cell Projection",
- HTML("scmap projects all cells
- of the Projection dataset to the
- reference calculated from the Reference dataset.
- The Reference is computed by calculating
- the median expression in each of 500
- selected features across all
- cells in each cell type."),
- solidHeader = TRUE,
- status = "primary"
- )
- ),
- conditionalPanel("input.data_type == 'existing'",
- box(width = 12,
- title = "Cell Projection",
- HTML("
scmap projects all cells
- of the Projection dataset to the precomputed
- References. The references were computed by
- selecting 500 most informative features of each
- Reference dataset and calculating
- the median expression in each of 500 features across all
- cells in each cell type."),
- solidHeader = TRUE,
- status = "primary"
- )
- )
+ box(width = 12,
+ title = "Cell Projection",
+ HTML("
scmap projects all cells
+ of the Projection dataset to the
+ either cell clusters (scmap-cluster) or
+ each individual cell (scmap-cell) of the Reference dataset."),
+ solidHeader = TRUE,
+ status = "primary"
+ )
),
- conditionalPanel(condition="!$('html').hasClass('shiny-busy') & output.scmap_cluster_worked",
- uiOutput("results_cluster")
+ conditionalPanel(condition="!$('html').hasClass('shiny-busy') & output.scmap_cluster_worked & output.scmap_cell_worked",
+ uiOutput("results")
),
conditionalPanel(condition="$('html').hasClass('shiny-busy')",
fluidRow(
@@ -252,11 +241,11 @@ dashboardPage(
offset = 2)
)
),
- conditionalPanel("!output.scmap_cluster_worked",
+ conditionalPanel("!output.scmap_cluster_worked || !output.scmap_cell_worked",
box(width = 12,
HTML("
-
scmap-cluster did not work! Most probably
+
scmap did not work! Most probably
Reference and Projection come from different organisms,
please check your inputs!