Code generator

[loguille]

Add code generator for each step of the workflow.
For the moment this pull request doesn't erase the code when the user goes rerun some previous step.

[leopoldguyot]

Could you add headers for the different steps ?
Something like this:

################################
####### Package Loading ########
################################
library(QFeatures)

#####################################
##### Step 1: Feature Filtering #####
#####################################
qf <- qf |> filterFeatures(~.qfeaturesgui_rowname != c('2'))

[leopoldguyot]

Also there is an issue when the user filter the features/samples by the rownames of the rowData/colData.
The internal accessor to the column that store this information in QFeaturesGUI will be used in the script:
qf <- qf |> filterFeatures(~.qfeaturesgui_rowname != c('2'))

[leopoldguyot]

# Reproducible R script
# Generated on: 2026-04-08 15:15:21.352928

library(QFeatures)

qf <- qf[, colData(qf)$SampleType != c("Unused", "Blank")] ## here it should use ! ... %in% c(...,)
qf <- qf |>
    filterFeatures(~ Potential.contaminant != c("+")) |>
    filterFeatures(~ Reverse != c("+")) |>
    filterFeatures(~ .qfeaturesgui_rowname != c("4"))
## normalize() can be use with a "i" parameter
qf <- lapply(names(qf), function(name) { ## This will apply the normalisation to all sets
    normalize(
        object = qf[[name]],
        method = "center.median"
    )
})
## aggregateFeatures can be use with a "i" parameter
qf <- lapply(seq_along(qf), function(i) {
    name <- names(qf)[i]
    aggregateFeatures(
        object = qf[[name]],
        method = colMedians,
        runCol = "Modified.sequence",
        na.rm = TRUE
    )
})
qf <- joinAssays(
    x = qf,
    i = names(qf)
    # it is missing the name specification
)
qf <- lapply(seq_along(qf), function(i) {
    name <- names(qf)[i]
    aggregateFeatures(
        object = qf[[name]],
        method = colMeans,
        runCol = "Leading.razor.protein",
        na.rm = TRUE
    )
})