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Updagte aggregation module
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@samWieczorek
samWieczorek committed Dec 10, 2024
1 parent 43a156b commit c59f246
Showing 1 changed file with 111 additions and 141 deletions.
252 changes: 111 additions & 141 deletions inst/workflow/PipelinePeptide/R/PipelinePeptide_Aggregation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,8 @@ PipelinePeptide_Aggregation_conf <- function(){
MagellanNTK::Config(
fullname = 'PipelinePeptide_Aggregation',
mode = 'process',
steps = c('Aggregation', 'Add metadata'),
mandatory = c(FALSE, FALSE)
steps = c('Aggregation'),
mandatory = c(TRUE)
)
}

Expand Down Expand Up @@ -95,6 +95,7 @@ PipelinePeptide_Aggregation_server <- function(id,
Aggregation_proteinId = "None",
Aggregation_topN = 3,
Aggregation_filterProtAfterAgregation = NULL,
Aggregation_addRowData = FALSE,
Addmetadata_columnsForProteinDataset = NULL
)

Expand Down Expand Up @@ -184,17 +185,6 @@ PipelinePeptide_Aggregation_server <- function(id,
observeEvent(input$Description_btn_validate, {
rv$dataIn <- dataIn()

## Build the adjacency matrix if they are not present
.data <- last_assay(rv$dataIn)
if (!("adjacencyMatrix" %in% names(rowData(.data)))){
QFeatures::adjacencyMatrix(rv$dataIn[[length(rv$dataIn)]]) <- BuildAdjacencyMatrix(.data, DaparToolshed::parentProtId(.data), FALSE)
}
rv.custom$X <- QFeatures::adjacencyMatrix(rv$dataIn[[length(rv$dataIn)]])
rv.custom$X.split <- DaparToolshed::splitAdjacencyMat(rv.custom$X)
rv.custom$X.shared <- rv.custom$X.split$Xshared
rv.custom$X.unique <- rv.custom$X.split$Xspec

print("Initialization finished")

dataOut$trigger <- MagellanNTK::Timestamp()
dataOut$value <- rv$dataIn
Expand Down Expand Up @@ -244,10 +234,12 @@ PipelinePeptide_Aggregation_server <- function(id,
div(style = .style,
uiOutput(ns('Aggregation_considerPeptides_ui'))
),

div(style = .style,
uiOutput(ns('Aggregation_operator_ui'))
)
),
div(style = .style,
uiOutput(ns('Aggregation_addRowData_ui'))
)
),
div(style = .style,
uiOutput(ns("Aggregation_btn_validate_ui"))
Expand Down Expand Up @@ -332,6 +324,13 @@ PipelinePeptide_Aggregation_server <- function(id,
})


output$Aggregation_addRowData_ui <- renderUI({
widget <- checkboxInput(ns("Aggregation_addRowData"), "Add rowData?",
value = rv.widgets$Aggregation_addRowData
)
MagellanNTK::toggleWidget(widget, rv$steps.enabled['Aggregation'])
})


output$Aggregation_operator_ui <- renderUI({

Expand Down Expand Up @@ -405,30 +404,72 @@ PipelinePeptide_Aggregation_server <- function(id,
incProgress(0.5, detail = "Aggregation in progress")

# Update the adjacency matrix to use
X <- NULL
if (rv.widgets$Aggregation_includeSharedPeptides %in% c("Yes2", "Yes1"))
X = rv.custom$X.shared
else
X = rv.custom$X.unique
# X <- NULL
# if (rv.widgets$Aggregation_includeSharedPeptides %in% c("Yes2", "Yes1"))
# X = rv.custom$X.shared
# else
# X = rv.custom$X.unique

i.last <- length(rv$dataIn)
#adjacencyMatrix(rv$dataIn[[i.last]]) <- X

feat1 <- aggregateFeatures4Prostar(
ll.agg <- aggregateFeatures4Prostar(
object = rv$dataIn,
i = i.last,
name = 'aggregated',
fcol = 'adjacencyMatrix',
fun = 'colSumsMat')

ll.agg <- NULL

})

return(ll.agg)
})


Add_Aggregated_rowData <- reactive({


req('aggregated' %in% names(rv.custom$temp.aggregate))


# Add aggregated simple columns rowData
total <- 60

i.agg <- length(rv.custom$temp.aggregate)
i.before.agg <- i.agg - 1
.names <- names(rowData(rv.custom$temp.aggregate[[i.before.agg]]))
.names <- .names[-match(c('qMetacell', 'adjacencyMatrix'), .names)]

delta <- round(total / length(.names))
cpt <- 10

withProgress(message = "", detail = "", value = 0, {
incProgress(0.5, detail = "Aggregation in progress")

for (col.name in .names) {
#browser()

newCol <- BuildColumnToProteinDataset(
peptideData = rowData((rv.custom$temp.aggregate[[i.agg - 1]])),
matAdj = rv.custom$X,
columnName = col.name,
proteinNames = rownames(rowData((rv.custom$temp.aggregate[[i.agg]])))
)
#browser()
cnames <- colnames(rowData(rv.custom$temp.aggregate[[i.agg]]))
rowData(rv.custom$temp.aggregate[[i.agg]]) <-
data.frame(rowData(rv.custom$temp.aggregate[[i.agg]]), newCol)

colnames(rowData(rv.custom$temp.aggregate[[i.agg]])) <- c(
cnames,
paste0("agg_", col.name)
)

cpt <- cpt + delta
incProgress(cpt / 100, detail = paste0("Processing column ", col.name))
}
})
})


output$Aggregation_AggregationDone_ui <- renderUI({
req(rv.custom$temp.aggregate)

Expand Down Expand Up @@ -497,93 +538,43 @@ PipelinePeptide_Aggregation_server <- function(id,

})

observeEvent(input$Aggregation_btn_validate, {
# Do some stuff
rv.custom$temp.aggregate <- RunAggregation()

# DO NOT MODIFY THE THREE FOLLOWINF LINES
dataOut$trigger <- MagellanNTK::Timestamp()
dataOut$value <- NULL
rv$steps.status['Aggregation'] <- is.null(rv.custom$temp.aggregate$issues)
#rv$steps.status['Aggregation'] <- stepStatus$VALIDATED
})

# <<< END ------------- Code for step 1 UI---------------





# >>>
# >>> START ------------- Code for Aggregation UI---------------
# >>>

# >>>> -------------------- STEP 1 : Global UI -----------------
output$Addmetadata <- renderUI({
shinyjs::useShinyjs()
BiuldAdjacencyMatrix <- reactive({

wellPanel(
# uiOutput for all widgets in this UI
# This part is mandatory
# The renderUlength(rv$dataIn) function of each widget is managed by MagellanNTK
# The dev only have to define a reactive() function for each
# widget he want to insert
# Be aware of the naming convention for ids in uiOutput()
# For more details, please refer to the dev document.

uiOutput("Addmetadata_displayNbPeptides_ui"),
#popover_for_help_ui("modulePopover_colsForAggreg"),
uiOutput("Addmetadata_columnsForProteinDataset_ui")
)
})


output$Addmetadata_displayNbPeptides_ui <- renderUI({


})



output$Addmetadata_columnsForProteinDataset_ui <- renderUI({
req(rv$dataIn)

## Build the adjacency matrix if they are not present
.data <- last_assay(rv$dataIn)
ind <- match(
colnames(qMetacell(.data)), .colnames)
.colnames <- colnames(rowData(.data))
choices <- setNames(nm = .colnames[-ind])
widget <- selectInput(ns("Addmetadata_columnsForProteinDataset"),
label = "",
choices = choices,
multiple = TRUE,
width = "200px",
selectize = TRUE
)
if (!("adjacencyMatrix" %in% names(rowData(.data)))){
withProgress(message = "", detail = "", value = 0, {
incProgress(0.5, detail = "Build the adjacency matrix")
QFeatures::adjacencyMatrix(rv$dataIn[[length(rv$dataIn)]]) <- BuildAdjacencyMatrix(.data, DaparToolshed::parentProtId(.data), FALSE)
})
}
rv.custom$X <- QFeatures::adjacencyMatrix(rv$dataIn[[length(rv$dataIn)]])
rv.custom$X.split <- DaparToolshed::splitAdjacencyMat(rv.custom$X)
rv.custom$X.shared <- rv.custom$X.split$Xshared
rv.custom$X.unique <- rv.custom$X.split$Xspec

print("Initialization finished")

MagellanNTK::toggleWidget(widget, rv$steps.enabled['Addmetadata'] )
})





output$Addmetadata_btn_validate_ui <- renderUI({
widget <- actionButton(ns("Addmetadata_btn_validate"),
"Validate step",
class = "btn-success")
MagellanNTK::toggleWidget(widget, rv$steps.enabled['Addmetadata'] )

})
observeEvent(input$Aggregation_btn_validate, {


BuildAdjacencyMatrix()
# Do some stuff
rv.custom$temp.aggregate <- RunAggregation()

if (rv.widgets$Aggregation_addRowData)
rv.custom$temp.aggregate <- Add_Aggregated_rowData()

# DO NOT MODIFY THE THREE FOLLOWINF LINES
dataOut$trigger <- MagellanNTK::Timestamp()
dataOut$value <- NULL
#rv$steps.status['Aggregation'] <- is.null(rv.custom$temp.aggregate$issues)

observeEvent(input$Addmetadata_btn_validate, {
# Do some stuff
rv.custom$temp.aggregate <- RunAggregation()

# DO NOT MODIFY THE THREE FOLLOWINF LINES
dataOut$trigger <- MagellanNTK::Timestamp()
dataOut$value <- NULL
rv$steps.status['Aggregation'] <- stepStatus$VALIDATED
})

Expand Down Expand Up @@ -617,7 +608,8 @@ observeEvent(input$Addmetadata_btn_validate, {
observeEvent(input$Save_btn_validate, {
# Do some stuff

# req(rv.custom$temp.aggregate$obj.prot)
req(rv.custom$temp.aggregate)

# req(is.null(rv.custom$temp.aggregate$issues))
#
# .data <- last_assay(rv$dataIn)
Expand All @@ -633,46 +625,24 @@ observeEvent(input$Addmetadata_btn_validate, {
# X <- rv.custom$X.unique
# }
#
# total <- 60
#
# delta <- round(total / length(rv.widgets$Addmetadata_columnsForProteinDataset))
# cpt <- 10
#
# for (c in rv.widgets$Addmetadata_columnsForProteinDataset) {
# newCol <- BuildColumnToProteinDataset(
# peptideData = rowData(.data),
# matAdj = rv.custom$X,
# columnName = c,
# proteinNames = rownames(rowData((rv.custom$temp.aggregate$obj.prot)))
# )
# cnames <- colnames(rowData(rv.custom$temp.aggregate$obj.prot))
# rowData(rv.custom$temp.aggregate$obj.prot) <-
# data.frame(rowData(rv.custom$temp.aggregate$obj.prot), newCol)
#
# colnames(rowData(rv.custom$temp.aggregate$obj.prot)) <- c(
# cnames,
# paste0("agg_", c)
# )
#
# cpt <- cpt + delta
# incProgress(cpt / 100, detail = paste0("Processing column ", c))
# }
#
# rv.custom$history[['Aggregation_includeSharedPeptides']] <- as.numeric(rv.widgets$Aggregation_includeSharedPeptides)
# rv.custom$history[['Aggregation_operator']] <- as.numeric(rv.widgets$Aggregation_operator)
# rv.custom$history[['Aggregation_considerPeptides']] <- as.numeric(rv.widgets$Aggregation_considerPeptides)
# rv.custom$history[['Aggregation_proteinId']] <- as.numeric(rv.widgets$Aggregation_proteinId)
# rv.custom$history[['Aggregation_topN']] <- as.numeric(rv.widgets$Aggregation_topN)
# rv.custom$history[['Aggregation_filterProtAfterAgregation']] <- as.numeric(rv.widgets$Aggregation_filterProtAfterAgregation)
# rv.custom$history[['Addmetadata_columnsForProteinDataset']] <- as.numeric(rv.widgets$Addmetadata_columnsForProteinDataset)
#
# paramshistory(new.dataset) <- rv.custom$history
#


rv.custom$history[['Aggregation_includeSharedPeptides']] <- as.numeric(rv.widgets$Aggregation_includeSharedPeptides)
rv.custom$history[['Aggregation_operator']] <- as.numeric(rv.widgets$Aggregation_operator)
rv.custom$history[['Aggregation_considerPeptides']] <- as.numeric(rv.widgets$Aggregation_considerPeptides)
rv.custom$history[['Aggregation_proteinId']] <- as.numeric(rv.widgets$Aggregation_proteinId)
rv.custom$history[['Aggregation_topN']] <- as.numeric(rv.widgets$Aggregation_topN)
rv.custom$history[['Aggregation_filterProtAfterAgregation']] <- as.numeric(rv.widgets$Aggregation_filterProtAfterAgregation)
rv.custom$history[['Aggregation_addRowData']] <- rv.widgets$Aggregation_addRowData

paramshistory(rv.custom$temp.aggregate[[length(rv.custom$temp.aggregate)]]) <- rv.custom$history

browser()
# new.dataset <- rv$temp.aggregate$obj.prot
#
# new.name <- paste0("Aggregated", ".", TypeOfDataset(new.dataset))
#
# rv$dataIn <- QFeatures::addAssay(rv$dataIn, new.dataset, new.name)
#

# DO NOT MODIFY THE THREE FOLLOWING LINES
dataOut$trigger <- MagellanNTK::Timestamp()
Expand Down

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