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Merged
rroutsong merged 2 commits into from
May 12, 2026
Merged

feat: module score page #6

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a590366
feat: module score page
rroutsong May 11, 2026
306c554
fix: make seed closed
May 12, 2026
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7 changes: 7 additions & 0 deletions R/makeShinyCodes.R
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,7 @@ makeShinyCodes <- function(
readr::write_file(wrSVmainB1(i), file = fname, append = TRUE)
readr::write_file(wrSVmainB2(i), file = fname, append = TRUE)
readr::write_file(wrSVmainB3(i), file = fname, append = TRUE)
readr::write_file(wrSVmainMOD(i), file = fname, append = TRUE)
}
readr::write_file(wrSVpost(), file = fname, append = TRUE)

Expand Down Expand Up @@ -156,6 +157,7 @@ makeShinyCodes <- function(
readr::write_file(wrUImainB1(shiny.prefix, defPtSiz[1]), file = fname, append = TRUE)
readr::write_file(wrUImainB2(shiny.prefix), file = fname, append = TRUE)
readr::write_file(wrUImainB3(shiny.prefix), file = fname, append = TRUE)
readr::write_file(wrUImainMOD(shiny.prefix), file = fname, append = TRUE)
readr::write_file(glue::glue(', \n'), append = TRUE, file = fname)
} else {
for (i in seq_along(shiny.prefix)) {
Expand Down Expand Up @@ -223,6 +225,11 @@ makeShinyCodes <- function(
file = fname,
append = TRUE
)
readr::write_file(
wrUImainMOD(shiny.prefix[i]),
file = fname,
append = TRUE
)
readr::write_file(glue::glue('), \n\n\n'), append = TRUE, file = fname)
}
}
Expand Down
22 changes: 21 additions & 1 deletion R/writer0.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1293,7 +1293,27 @@ wrShFunc <- function() {
' }}\n',
' return(ggOut)\n',
'}}\n',
'\n',
'\n',
'\n',
'\n',
'## Module score helper function \n',
'scModuleScore <- function(inpGene, inpH5, geneList, seed = 42) {{\n',
' valid <- geneList[present == TRUE]$gene\n',
' bgPool <- setdiff(names(inpGene), valid)\n',
' set.seed(seed)\n',
' bgGenes <- sample(bgPool, min(length(valid), length(bgPool)))\n',
' h5file <- H5File$new(inpH5, mode = "r")\n',
' h5data <- h5file[["grp"]][["data"]]\n',
' readRows <- function(genes) {{\n',
' do.call(rbind, lapply(genes, function(g)\n',
' pmax(h5data$read(args = list(inpGene[g], quote(expr=))), 0)))\n',
' }}\n',
' targetMat <- readRows(valid)\n',
' bgMat <- readRows(bgGenes)\n',
' h5file$close_all()\n',
' colMeans(targetMat) - colMeans(bgMat)\n',
'}}\n',
'\n',
'\n',
'\n'
)
Expand Down
168 changes: 168 additions & 0 deletions R/writer1.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1519,6 +1519,174 @@ wrSVmainT1 <- function(prefix) {
)
}

#' Write code for server.R - Module Score tab
#'
#' @rdname wrSVmainMOD
#' @export wrSVmainMOD
#'
wrSVmainMOD <- function(prefix) {
glue::glue(
' ### Functions for Module Score tab \n',
' output${prefix}comb_sub1.ui <- renderUI({{ \n',
' sub = strsplit({prefix}conf[UI == input${prefix}comb_sub1]$fID, "\\\\|")[[1]] \n',
' checkboxGroupInput("{prefix}comb_sub2", "Select which cells to show", inline = TRUE, \n',
' choices = sub, selected = sub) \n',
' }}) \n',
' observeEvent(input${prefix}comb_sub1non, {{ \n',
' sub = strsplit({prefix}conf[UI == input${prefix}comb_sub1]$fID, "\\\\|")[[1]] \n',
' updateCheckboxGroupInput(session, inputId = "{prefix}comb_sub2", \n',
' choices = sub, selected = NULL, inline = TRUE) \n',
' }}) \n',
' observeEvent(input${prefix}comb_sub1all, {{ \n',
' sub = strsplit({prefix}conf[UI == input${prefix}comb_sub1]$fID, "\\\\|")[[1]] \n',
' updateCheckboxGroupInput(session, inputId = "{prefix}comb_sub2", \n',
' choices = sub, selected = sub, inline = TRUE) \n',
' }}) \n',
'\n',
' output${prefix}comb_mod_geneTxt <- renderUI({{ \n',
' geneList <- scGeneList(input${prefix}comb_mod_inp, {prefix}gene[[input${prefix}comb_mod_ass]]) \n',
' if (nrow(geneList) > 50) {{ \n',
' HTML("<span style=\'color:red\'>More than 50 genes! Please reduce the list.</span>") \n',
' }} else {{ \n',
' ok <- nrow(geneList[present == TRUE]) \n',
' bad <- nrow(geneList[present == FALSE]) \n',
' oup <- paste0(ok, " genes found and will be used for scoring") \n',
' if (bad > 0) \n',
' oup <- paste0(oup, "<br/><span style=\'color:orange\'>", bad, " not found: ", \n',
' paste0(geneList[present == FALSE]$gene, collapse = ", "), "</span>") \n',
' HTML(oup) \n',
' }} \n',
' }}) \n',
'\n',
' {prefix}comb_mod_score <- reactive({{ \n',
' geneList <- scGeneList(input${prefix}comb_mod_inp, {prefix}gene[[input${prefix}comb_mod_ass]]) \n',
' shiny::validate( \n',
' need(nrow(geneList[present == TRUE]) >= 2, \n',
' "Please provide at least 2 valid genes."), \n',
' need(nrow(geneList) <= 50, \n',
' "More than 50 genes - please reduce the list.") \n',
' ) \n',
' inpH5 <- paste0("{prefix}assay_", input${prefix}comb_mod_ass, ".h5") \n',
' scModuleScore({prefix}gene[[input${prefix}comb_mod_ass]], inpH5, geneList, \n',
' seed = 42) \n',
' }}) \n',
'\n',
' {prefix}comb_mod_dr_oup <- reactive({{ \n',
' score <- {prefix}comb_mod_score() \n',
' inpdr <- input${prefix}comb_mod_dr \n',
' ggData <- data.table({prefix}dimr[[inpdr]]); colnames(ggData) <- c("X","Y") \n',
' rat <- (max(ggData$X) - min(ggData$X)) / (max(ggData$Y) - min(ggData$Y)) \n',
' sub1 <- if (is.null(input${prefix}comb_sub1)) {prefix}conf$UI[1] else input${prefix}comb_sub1 \n',
' ggData$sub <- {prefix}meta[, {prefix}conf[UI == sub1]$ID, with = FALSE][[1]] \n',
' ggData$val <- score \n',
' bgCells <- FALSE \n',
' if (length(input${prefix}comb_sub2) != 0 && \n',
' length(input${prefix}comb_sub2) != nlevels(ggData$sub)) {{ \n',
' bgCells <- TRUE \n',
' ggData2 <- ggData[!sub %in% input${prefix}comb_sub2] \n',
' ggData <- ggData[sub %in% input${prefix}comb_sub2] \n',
' }} \n',
' if (input${prefix}comb_mod_ord == "Max-1st") {{ \n',
' ggData <- ggData[order(val)] \n',
' }} else if (input${prefix}comb_mod_ord == "Min-1st") {{ \n',
' ggData <- ggData[order(-val)] \n',
' }} else if (input${prefix}comb_mod_ord == "Random") {{ \n',
' ggData <- ggData[sample(nrow(ggData))] \n',
' }} \n',
' inpfsz <- sList[input${prefix}comb_mod_fsz] \n',
' inpcol <- cList[[input${prefix}comb_mod_col]] \n',
' ggOut <- ggplot(ggData, aes(X, Y, color = val)) \n',
' if (bgCells) \n',
' ggOut <- ggOut + geom_point(data = ggData2, color = "snow2", \n',
' size = input${prefix}comb_mod_siz / 2, shape = 16) \n',
' ggOut <- ggOut + \n',
' geom_point(size = input${prefix}comb_mod_siz, shape = 16) + \n',
' xlab(paste0(inpdr,"1")) + ylab(paste0(inpdr,"2")) + \n',
' sctheme(base_size = inpfsz, XYval = input${prefix}comb_mod_txt) + \n',
' scale_color_gradientn("Module Score ", colours = inpcol) + \n',
' guides(color = guide_colorbar(barwidth = 15)) \n',
' asp <- input${prefix}comb_mod_asp \n',
' if (asp == "Square") ggOut <- ggOut + coord_fixed(ratio = 1) \n',
' else if (asp == "Fixed") ggOut <- ggOut + coord_fixed(ratio = rat) \n',
' ggOut \n',
' }}) \n',
' output${prefix}comb_mod_dr_oup.ui <- renderUI({{ \n',
' plotOutput("{prefix}comb_mod_dr_oup", height = pList[input${prefix}comb_mod_psz]) \n',
' }}) \n',
' output${prefix}comb_mod_dr_oup <- renderPlot({{ \n',
' {prefix}comb_mod_dr_oup() + theme(legend.position = "none") \n',
' }}) \n',
' output${prefix}comb_mod_leg_oup.ui <- renderUI({{ \n',
' plotOutput("{prefix}comb_mod_leg_oup", \n',
' height = 72 * convertHeight( \n',
' grobHeight(g_legend({prefix}comb_mod_dr_oup())), \n',
' unitTo = "in", valueOnly = TRUE) + 50) \n',
' }}) \n',
' output${prefix}comb_mod_leg_oup <- renderPlot({{ \n',
' grid.newpage(); grid.draw(g_legend({prefix}comb_mod_dr_oup())) \n',
' }}) \n',
' output${prefix}comb_mod_dr_oup.dl <- downloadHandler( \n',
' filename = function() {{ \n',
' paste0("{prefix}modscore_dimred_", input${prefix}comb_mod_dr, \n',
' ".", input${prefix}comb_mod_dr_oup.f) \n',
' }}, \n',
' content = function(file) {{ \n',
' p <- {prefix}comb_mod_dr_oup() + theme(legend.position = "none") \n',
' ggsav(file, height = input${prefix}comb_mod_dr_oup.h, \n',
' width = input${prefix}comb_mod_dr_oup.w, plot = p) \n',
' }} \n',
' ) \n',
'\n',
' {prefix}comb_mod_vln_oup <- reactive({{ \n',
' score <- {prefix}comb_mod_score() \n',
' sub1 <- if (is.null(input${prefix}comb_sub1)) {prefix}conf$UI[1] else input${prefix}comb_sub1 \n',
' ggData <- data.table( \n',
' X = {prefix}meta[, {prefix}conf[UI == input${prefix}comb_grp]$ID, with = FALSE][[1]], \n',
' sub = {prefix}meta[, {prefix}conf[UI == sub1]$ID, with = FALSE][[1]], \n',
' val = score \n',
' ) \n',
' if (length(input${prefix}comb_sub2) != 0 && \n',
' length(input${prefix}comb_sub2) != nlevels(ggData$sub)) \n',
' ggData <- ggData[sub %in% input${prefix}comb_sub2] \n',
' ggCol <- strsplit({prefix}conf[UI == input${prefix}comb_grp]$fCL, "\\\\|")[[1]] \n',
' names(ggCol) <- levels(ggData$X) \n',
' ggLvl <- levels(ggData$X)[levels(ggData$X) %in% unique(ggData$X)] \n',
' ggData$X <- factor(ggData$X, levels = ggLvl) \n',
' ggCol <- ggCol[ggLvl] \n',
' inpfsz <- sList[input${prefix}comb_mod_fsz] \n',
' if (input${prefix}comb_mod_vln_typ == "violin") {{ \n',
' ggOut <- ggplot(ggData, aes(X, val, fill = X)) + geom_violin(scale = "width") \n',
' }} else {{ \n',
' ggOut <- ggplot(ggData, aes(X, val, fill = X)) + geom_boxplot() \n',
' }} \n',
' if (input${prefix}comb_mod_vln_pts) \n',
' ggOut <- ggOut + geom_jitter(size = input${prefix}comb_mod_siz, shape = 16) \n',
' ggOut + \n',
' xlab(input${prefix}comb_grp) + ylab("Module Score") + \n',
' sctheme(base_size = inpfsz, Xang = 45, XjusH = 1) + \n',
' scale_fill_manual("", values = ggCol) + \n',
' theme(legend.position = "none") \n',
' }}) \n',
' output${prefix}comb_mod_vln_oup.ui <- renderUI({{ \n',
' plotOutput("{prefix}comb_mod_vln_oup", height = pList2[input${prefix}comb_mod_psz]) \n',
' }}) \n',
' output${prefix}comb_mod_vln_oup <- renderPlot({{{prefix}comb_mod_vln_oup()}}) \n',
' output${prefix}comb_mod_vln_oup.dl <- downloadHandler( \n',
' filename = function() {{ \n',
' paste0("{prefix}modscore_violin_", input${prefix}comb_grp, \n',
' ".", input${prefix}comb_mod_vln_oup.f) \n',
' }}, \n',
' content = function(file) {{ \n',
' ggsav(file, height = input${prefix}comb_mod_vln_oup.h, \n',
' width = input${prefix}comb_mod_vln_oup.w, plot = {prefix}comb_mod_vln_oup()) \n',
' }} \n',
' ) \n',
'\n',
'\n',
'\n'
)
}

#' Write code for server.R
#'
#' @rdname wrSVpost
Expand Down
122 changes: 122 additions & 0 deletions R/writer2.R
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Expand Up @@ -1076,6 +1076,128 @@ wrUImainB3 <- function(prefix) {
)
}

#' Write code for ui.R - Module Score tab
#'
#' @rdname wrUImainMOD
#' @export wrUImainMOD
#'
wrUImainMOD <- function(prefix) {
glue::glue(
' ### Tab: Module scoring \n',
' tabPanel( \n',
' HTML("Module scoring"), \n',
' h4("Gene Module Score: Violin + Dimred"), \n',
' "Compute a per-cell module score (mean expression of a gene list minus the mean of ", \n',
' "a random background gene set of equal size), then visualise across cell groups ", \n',
' "and on a reduced-dimension plot.", \n',
' br(), br(), \n',
' fluidRow( \n',
' column( \n',
' 4, \n',
' selectInput("{prefix}comb_grp", "Group by:", \n',
' choices = {prefix}conf[grp == TRUE]$UI, \n',
' selected = {prefix}def$grp1) \n',
' ), \n',
' column( \n',
' 4, \n',
' actionButton("{prefix}comb_togL", "Toggle to subset cells"), \n',
' conditionalPanel( \n',
' condition = "input.{prefix}comb_togL % 2 == 1", \n',
' selectInput("{prefix}comb_sub1", "Cell information to subset:", \n',
' choices = {prefix}conf[grp == TRUE]$UI, \n',
' selected = {prefix}def$grp1), \n',
' uiOutput("{prefix}comb_sub1.ui"), \n',
' actionButton("{prefix}comb_sub1all", "Select all groups", class = "btn btn-primary"), \n',
' actionButton("{prefix}comb_sub1non", "Deselect all groups", class = "btn btn-primary") \n',
' ) \n',
' ) \n',
' ), \n',
' fluidRow( \n',
' column( \n',
' 3, style = "border-right: 2px solid black", \n',
' textAreaInput("{prefix}comb_mod_inp", \n',
' HTML("Gene list for module score<br/>(max 50, separated by , ; or newline):"), \n',
' height = "200px", \n',
' value = paste0({prefix}def$genes[[1]], collapse = ", ")) %>% \n',
' helper(type = "inline", size = "m", fade = TRUE, \n',
' title = "Genes for module score", \n',
' content = c("Input target genes to score per cell", \n',
' "- Score = mean(target genes) - mean(random background genes)", \n',
' "- Background pool size equals the target gene list size", \n',
' "- Separate genes by comma, semicolon, or newline")), \n',
' selectInput("{prefix}comb_mod_ass", "Assay:", \n',
' choices = {prefix}def$assay, \n',
' selected = {prefix}def$assay[1]), \n',
' h4(htmlOutput("{prefix}comb_mod_geneTxt")), \n',
' br(), \n',
' actionButton("{prefix}comb_mod_tog", "Toggle graphics controls"), \n',
' conditionalPanel( \n',
' condition = "input.{prefix}comb_mod_tog % 2 == 1", \n',
' sliderInput("{prefix}comb_mod_siz", "Point size:", \n',
' min = 0, max = 4, value = 1.25, step = 0.25), \n',
' radioButtons("{prefix}comb_mod_psz", "Plot size:", \n',
' choices = c("Small", "Medium", "Large"), \n',
' selected = "Medium", inline = TRUE), \n',
' radioButtons("{prefix}comb_mod_fsz", "Font size:", \n',
' choices = c("Small", "Medium", "Large"), \n',
' selected = "Medium", inline = TRUE), \n',
' radioButtons("{prefix}comb_mod_col", "Dimred colour palette:", \n',
' choices = c("White-Red", "Blue-Yellow-Red", "Yellow-Green-Purple"), \n',
' selected = "Blue-Yellow-Red"), \n',
' radioButtons("{prefix}comb_mod_dr", "Reduction:", \n',
' choices = {prefix}def$dimrd, \n',
' selected = {prefix}def$dimrd[1]), \n',
' radioButtons("{prefix}comb_mod_asp", "Aspect ratio:", \n',
' choices = c("Square", "Fixed", "Free"), \n',
' selected = "Square", inline = TRUE), \n',
' checkboxInput("{prefix}comb_mod_txt", "Show axis text on dimred", value = FALSE), \n',
' radioButtons("{prefix}comb_mod_ord", "Dimred plot order:", \n',
' choices = c("Max-1st", "Min-1st", "Original", "Random"), \n',
' selected = "Max-1st", inline = TRUE), \n',
' radioButtons("{prefix}comb_mod_vln_typ", "Violin/boxplot type:", \n',
' choices = c("violin", "boxplot"), \n',
' selected = "violin", inline = TRUE), \n',
' checkboxInput("{prefix}comb_mod_vln_pts", "Show data points on violin", value = FALSE) \n',
' ) \n',
' ), \n',
' column( \n',
' 5, style = "border-right: 2px solid black", \n',
' h4("Module score on reduced dimensions"), \n',
' uiOutput("{prefix}comb_mod_dr_oup.ui"), \n',
' fluidRow(column(6, uiOutput("{prefix}comb_mod_leg_oup.ui"))), \n',
' fluidRow( \n',
' column(3, downloadButton("{prefix}comb_mod_dr_oup.dl", "Download")), \n',
' column(3, radioButtons("{prefix}comb_mod_dr_oup.f", "Format:", \n',
' choices = c("png", "pdf"), selected = "png", inline = TRUE)), \n',
' column(3, numericInput("{prefix}comb_mod_dr_oup.h", "Height:", \n',
' min = 4, max = 20, value = 8, step = 0.5)), \n',
' column(3, numericInput("{prefix}comb_mod_dr_oup.w", "Width:", \n',
' min = 4, max = 20, value = 8, step = 0.5)) \n',
' ), \n',
' br() \n',
' ), \n',
' column( \n',
' 4, \n',
' h4("Module score violin / boxplot"), \n',
' uiOutput("{prefix}comb_mod_vln_oup.ui"), \n',
' fluidRow( \n',
' column(3, downloadButton("{prefix}comb_mod_vln_oup.dl", "Download")), \n',
' column(3, radioButtons("{prefix}comb_mod_vln_oup.f", "Format:", \n',
' choices = c("png", "pdf"), selected = "png", inline = TRUE)), \n',
' column(3, numericInput("{prefix}comb_mod_vln_oup.h", "Height:", \n',
' min = 4, max = 20, value = 8, step = 0.5)), \n',
' column(3, numericInput("{prefix}comb_mod_vln_oup.w", "Width:", \n',
' min = 4, max = 20, value = 8, step = 0.5)) \n',
' ), \n',
' br() \n',
' ) \n',
' ) # End of fluidRow (4 space) \n',
' ) # End of tab (2 space) \n',
' , \n',
' \n'
)
}

#' Write code for ui.R
#'
#' @rdname wrUImainS1
Expand Down
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