--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_facets_enhanced-v22.R	Sun Oct 05 00:55:34 2025 +0000
@@ -0,0 +1,263 @@
+plot_facets_enhanced <- function(x, emfit = NULL, clustered = FALSE,
+                                 plot.type = c("em", "naive", "both", "none"),
+                                 sname = NULL, add.legend = TRUE) {
+    def.par <- par(no.readonly = TRUE)
+    plot.type <- match.arg(plot.type)
+
+    # Setup layout
+    if (plot.type == "none") {
+        layout(matrix(1:2, ncol = 1))
+    }
+    if (plot.type == "em") {
+        layout(matrix(rep(1:4, c(9, 9, 6, 1)), ncol = 1))
+    }
+    if (plot.type == "naive") {
+        layout(matrix(rep(1:4, c(9, 9, 6, 1)), ncol = 1))
+    }
+    if (plot.type == "both") {
+        layout(matrix(rep(1:6, c(9, 9, 6, 1, 6, 1)), ncol = 1))
+    }
+
+    par(
+        mar = c(0.25, 3, 0.25, 1), mgp = c(1.75, 0.6, 0),
+        oma = c(3, 0, 1.25, 0)
+    )
+
+    # Prepare data
+    jseg <- x$jointseg
+    chrbdry <- which(diff(jseg$chrom) != 0)
+
+    if (missing(emfit)) {
+        out <- x$out
+        if (plot.type == "em" | plot.type == "both") {
+            warning("emfit is missing; plot.type set to naive")
+            plot.type <- "naive"
+        }
+    } else {
+        out <- emfit$cncf
+        out$tcn <- x$out$tcn
+        out$lcn <- x$out$lcn
+        out$cf <- x$out$cf
+    }
+
+    if (clustered) {
+        cnlr.median <- out$cnlr.median.clust
+        mafR <- out$mafR.clust
+        mafR[is.na(mafR)] <- out$mafR[is.na(mafR)]
+    } else {
+        cnlr.median <- out$cnlr.median
+        mafR <- out$mafR
+    }
+
+    mafR <- abs(mafR)
+    chrcol <- 1 + rep(out$chrom - 2 * floor(out$chrom / 2), out$num.mark)
+    nn <- cumsum(table(jseg$chrom[is.finite(jseg$cnlr)]))
+    segbdry <- cumsum(c(0, out$num.mark))
+    segstart <- segbdry[-length(segbdry)]
+    segend <- segbdry[-1]
+
+    # Plot 1: log-ratio
+    plot(jseg$cnlr[is.finite(jseg$cnlr)],
+        pch = ".", cex = 2,
+        col = c("grey", "lightblue", "azure4", "slateblue")[chrcol],
+        ylab = "log-ratio", xaxt = "n"
+    )
+    abline(v = chrbdry, lwd = 0.25)
+
+    # Calculate reference lines
+    global_median <- median(jseg$cnlr, na.rm = TRUE)
+    diploid_logr <- x$dipLogR
+    lines_diff <- abs(global_median - diploid_logr)
+
+    # Only show reference lines if they are sufficiently different (> 0.1)
+    legend_items <- c("Segments")
+    legend_cols <- c(2)
+    legend_lwd <- c(1.75)
+    legend_lty <- c(1)
+
+    if (lines_diff > 0.1) {
+        # Lines are different enough to show both
+        abline(h = global_median, col = "green2", lwd = 2.5)
+        abline(h = diploid_logr, col = "magenta4", lwd = 2.5, lty = 2)
+        legend_items <- c(
+            legend_items,
+            sprintf("Global median (%.3f)", global_median),
+            sprintf("Diploid LogR (%.3f)", diploid_logr)
+        )
+        legend_cols <- c(legend_cols, "green2", "magenta4")
+        legend_lwd <- c(legend_lwd, 2.5, 2.5)
+        legend_lty <- c(legend_lty, 1, 2)
+    } else {
+        # Lines are too close, show only one with combined label
+        abline(h = global_median, col = "green2", lwd = 2.5)
+        legend_items <- c(
+            legend_items,
+            sprintf("Median/Diploid (%.3f)", global_median)
+        )
+        legend_cols <- c(legend_cols, "green2")
+        legend_lwd <- c(legend_lwd, 2.5)
+        legend_lty <- c(legend_lty, 1)
+    }
+
+    segments(segstart, cnlr.median, segend, cnlr.median, lwd = 1.75, col = 2)
+
+    # Add legend for log-ratio plot
+    if (add.legend) {
+        legend("topright",
+            legend = legend_items,
+            col = legend_cols,
+            lwd = legend_lwd,
+            lty = legend_lty,
+            bty = "n",
+            cex = 0.7
+        )
+    }
+
+    # Plot 2: log-odds-ratio
+    plot(jseg$valor[is.finite(jseg$cnlr)],
+        pch = ".", cex = 2.5,
+        col = c("grey", "lightblue", "azure4", "slateblue")[chrcol],
+        ylab = "log-odds-ratio", ylim = c(-4, 4), xaxt = "n"
+    )
+    abline(v = chrbdry, lwd = 0.25)
+    segments(segstart, sqrt(mafR), segend, sqrt(mafR), lwd = 1.75, col = 2)
+    segments(segstart, -sqrt(mafR), segend, -sqrt(mafR), lwd = 1.75, col = 2)
+
+    # Add legend for log-odds-ratio plot
+    if (add.legend) {
+        legend("topright",
+            legend = c("BAF segments"),
+            col = c(2),
+            lwd = c(1.75),
+            bty = "n",
+            cex = 0.7
+        )
+    }
+
+    cfpalette <- c(colorRampPalette(c("white", "steelblue"))(10), "bisque2")
+
+    # Plot 3: copy number (naive)
+    if (plot.type == "naive" | plot.type == "both") {
+        out$tcn[out$tcn > 10] <- 9 + log10(out$tcn[out$tcn > 10])
+        ii <- which(out$lcn > 5)
+        if (length(ii) > 0) {
+            out$lcn[ii] <- 5 + log10(out$lcn[ii])
+        }
+
+        plot(c(0, length(jseg$cnlr)), c(0, max(out$tcn)),
+            type = "n",
+            ylab = "copy number (nv)", xaxt = "n"
+        )
+        abline(v = chrbdry, lwd = 0.25)
+        segments(segstart, out$lcn, segend, out$lcn, lwd = 1.75, col = 2)
+        segments(segstart, out$tcn, segend, out$tcn, lwd = 1.75, col = 1)
+
+        # Add legends for copy number plot (including CF legend)
+        if (add.legend) {
+            # CN legend on top left
+            legend("topleft",
+                legend = c("Total CN (TCN)", "Minor CN (LCN)"),
+                col = c(1, 2),
+                lwd = 1.75,
+                bty = "n",
+                cex = 0.7
+            )
+
+            # CF legend on top right
+            legend("topright",
+                legend = c(
+                    "CF = 0 (normal)", "CF = 0.2 (low tumor)",
+                    "CF = 0.8 (high tumor)", "CF = 1.0 (pure tumor)"
+                ),
+                fill = c("white", "lightblue", "steelblue", "tan"),
+                border = "black",
+                bty = "o",
+                box.col = "black",
+                box.lwd = 1.5,
+                cex = 0.65,
+                title = "Cellular Fraction (CF)",
+                bg = "white"
+            )
+        }
+
+        # CF bar (naive)
+        plot(c(0, length(jseg$cnlr)), 0:1,
+            type = "n", ylab = "",
+            xaxt = "n", yaxt = "n"
+        )
+        mtext("cf-nv", side = 2, at = 0.5, line = 0.3, las = 2, cex = 0.75)
+        cfcol <- cfpalette[round(10 * out$cf + 0.501)]
+        rect(segstart, 0, segend, 1, col = cfcol, border = NA)
+    }
+
+    # Plot 4: copy number (EM)
+    if (plot.type == "em" | plot.type == "both") {
+        out$tcn.em[out$tcn.em > 10] <- 9 + log10(out$tcn.em[out$tcn.em > 10])
+        ii <- which(out$lcn.em > 5)
+        if (length(ii) > 0) {
+            out$lcn.em[ii] <- 5 + log10(out$lcn.em[ii])
+        }
+
+        plot(c(0, length(jseg$cnlr)), c(0, max(out$tcn.em)),
+            type = "n", ylab = "copy number (em)", xaxt = "n"
+        )
+        abline(v = chrbdry, lwd = 0.25)
+        segments(segstart, out$lcn.em, segend, out$lcn.em, lwd = 1.75, col = 2)
+        segments(segstart, out$tcn.em, segend, out$tcn.em, lwd = 1.75, col = 1)
+
+        # Add legends for EM copy number plot (including CF legend)
+        if (add.legend) {
+            # CN legend on top left
+            legend("topleft",
+                legend = c("Total CN (TCN)", "Minor CN (LCN)"),
+                col = c(1, 2),
+                lwd = 1.75,
+                bty = "n",
+                cex = 0.7
+            )
+
+            # CF legend on top right
+            legend("topright",
+                legend = c(
+                    "CF = 0 (normal)", "CF = 0.2 (low tumor)",
+                    "CF = 0.8 (high tumor)", "CF = 1.0 (pure tumor)"
+                ),
+                fill = c("white", "lightblue", "steelblue", "tan"),
+                border = "black",
+                bty = "o",
+                box.col = "black",
+                box.lwd = 1.5,
+                cex = 0.65,
+                title = "Cellular Fraction (CF)",
+                bg = "white"
+            )
+        }
+
+        # CF bar (EM)
+        plot(c(0, length(jseg$cnlr)), 0:1,
+            type = "n", ylab = "",
+            xaxt = "n", yaxt = "n"
+        )
+        mtext("cf-em", side = 2, at = 0.5, line = 0.2, las = 2, cex = 0.75)
+        cfcol <- cfpalette[round(10 * out$cf.em + 0.501)]
+        rect(segstart, 0, segend, 1, col = cfcol, border = NA)
+    }
+
+    # X-axis with chromosome labels
+    chromlevels <- x$chromlevels
+    if (is.null(chromlevels)) {
+        chromlevels <- 1:length(nn)
+    }
+    axis(
+        labels = chromlevels, side = 1,
+        at = (nn + c(0, nn[-length(nn)])) / 2, cex = 0.65
+    )
+    mtext(side = 1, line = 1.75, "Chromosome", cex = 0.8)
+
+    # Sample name title
+    if (!missing(sname)) {
+        mtext(sname, side = 3, line = 0, outer = TRUE, cex = 0.8)
+    }
+
+    par(def.par)
+}