Mercurial > repos > artbio > cnv_facets

annotate plot_facets_enhanced-v22.R @ 8:e8a8a4910e32 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 2a0f9aee1c61e12ab9f0e25a6ba7db5c08b67fe6
author artbio
date Thu, 09 Oct 2025 17:14:30 +0000
parents d1914f4d9daf
children
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d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
artbio
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1 plot_facets_enhanced <- function(x, emfit = NULL, clustered = FALSE,
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
artbio
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2 plot.type = c("em", "naive", "both", "none"),
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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3 sname = NULL, add.legend = TRUE) {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
artbio
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4 def.par <- par(no.readonly = TRUE)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
artbio
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5 plot.type <- match.arg(plot.type)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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6
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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7 # Setup layout
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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8 if (plot.type == "none") {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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9 layout(matrix(1:2, ncol = 1))
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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10 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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11 if (plot.type == "em") {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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12 layout(matrix(rep(1:4, c(9, 9, 6, 1)), ncol = 1))
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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13 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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14 if (plot.type == "naive") {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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15 layout(matrix(rep(1:4, c(9, 9, 6, 1)), ncol = 1))
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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16 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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17 if (plot.type == "both") {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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18 layout(matrix(rep(1:6, c(9, 9, 6, 1, 6, 1)), ncol = 1))
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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19 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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21 par(
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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22 mar = c(0.25, 3, 0.25, 1), mgp = c(1.75, 0.6, 0),
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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23 oma = c(3, 0, 1.25, 0)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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24 )
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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26 # Prepare data
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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27 jseg <- x$jointseg
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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28 chrbdry <- which(diff(jseg$chrom) != 0)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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29
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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30 if (missing(emfit)) {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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31 out <- x$out
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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32 if (plot.type == "em" | plot.type == "both") {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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33 warning("emfit is missing; plot.type set to naive")
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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34 plot.type <- "naive"
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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35 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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36 } else {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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37 out <- emfit$cncf
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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38 out$tcn <- x$out$tcn
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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39 out$lcn <- x$out$lcn
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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40 out$cf <- x$out$cf
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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41 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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42
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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43 if (clustered) {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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44 cnlr.median <- out$cnlr.median.clust
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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45 mafR <- out$mafR.clust
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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46 mafR[is.na(mafR)] <- out$mafR[is.na(mafR)]
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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47 } else {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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48 cnlr.median <- out$cnlr.median
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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49 mafR <- out$mafR
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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50 }
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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51
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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52 mafR <- abs(mafR)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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53 chrcol <- 1 + rep(out$chrom - 2 * floor(out$chrom / 2), out$num.mark)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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54 nn <- cumsum(table(jseg$chrom[is.finite(jseg$cnlr)]))
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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55 segbdry <- cumsum(c(0, out$num.mark))
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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56 segstart <- segbdry[-length(segbdry)]
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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57 segend <- segbdry[-1]
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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58
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59 # Plot 1: log-ratio
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60 plot(jseg$cnlr[is.finite(jseg$cnlr)],
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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61 pch = ".", cex = 2,
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62 col = c("grey", "lightblue", "azure4", "slateblue")[chrcol],
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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63 ylab = "log-ratio", xaxt = "n"
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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64 )
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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65 abline(v = chrbdry, lwd = 0.25)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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66
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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67 # Calculate reference lines
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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68 global_median <- median(jseg$cnlr, na.rm = TRUE)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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69 diploid_logr <- x$dipLogR
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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70 lines_diff <- abs(global_median - diploid_logr)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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71
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72 # Only show reference lines if they are sufficiently different (> 0.1)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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73 legend_items <- c("Segments")
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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74 legend_cols <- c(2)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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75 legend_lwd <- c(1.75)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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76 legend_lty <- c(1)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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77
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78 if (lines_diff > 0.1) {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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79 # Lines are different enough to show both
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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80 abline(h = global_median, col = "green2", lwd = 2.5)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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81 abline(h = diploid_logr, col = "magenta4", lwd = 2.5, lty = 2)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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82 legend_items <- c(
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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83 legend_items,
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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84 sprintf("Global median (%.3f)", global_median),
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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85 sprintf("Diploid LogR (%.3f)", diploid_logr)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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86 )
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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87 legend_cols <- c(legend_cols, "green2", "magenta4")
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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88 legend_lwd <- c(legend_lwd, 2.5, 2.5)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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89 legend_lty <- c(legend_lty, 1, 2)
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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90 } else {
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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91 # Lines are too close, show only one with combined label
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92 abline(h = global_median, col = "green2", lwd = 2.5)
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93 legend_items <- c(
d1914f4d9daf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
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94 legend_items,
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95 sprintf("Median/Diploid (%.3f)", global_median)
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96 )
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97 legend_cols <- c(legend_cols, "green2")
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98 legend_lwd <- c(legend_lwd, 2.5)
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99 legend_lty <- c(legend_lty, 1)
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100 }
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101
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102 segments(segstart, cnlr.median, segend, cnlr.median, lwd = 1.75, col = 2)
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103
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104 # Add legend for log-ratio plot
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105 if (add.legend) {
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106 legend("topright",
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107 legend = legend_items,
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108 col = legend_cols,
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109 lwd = legend_lwd,
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110 lty = legend_lty,
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111 bty = "n",
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112 cex = 0.7
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113 )
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114 }
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115
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116 # Plot 2: log-odds-ratio
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117 plot(jseg$valor[is.finite(jseg$cnlr)],
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118 pch = ".", cex = 2.5,
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119 col = c("grey", "lightblue", "azure4", "slateblue")[chrcol],
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120 ylab = "log-odds-ratio", ylim = c(-4, 4), xaxt = "n"
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121 )
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122 abline(v = chrbdry, lwd = 0.25)
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123 segments(segstart, sqrt(mafR), segend, sqrt(mafR), lwd = 1.75, col = 2)
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124 segments(segstart, -sqrt(mafR), segend, -sqrt(mafR), lwd = 1.75, col = 2)
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125
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126 # Add legend for log-odds-ratio plot
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127 if (add.legend) {
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128 legend("topright",
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129 legend = c("BAF segments"),
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130 col = c(2),
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131 lwd = c(1.75),
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132 bty = "n",
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133 cex = 0.7
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134 )
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135 }
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136
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137 cfpalette <- c(colorRampPalette(c("white", "steelblue"))(10), "bisque2")
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138
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139 # Plot 3: copy number (naive)
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140 if (plot.type == "naive" | plot.type == "both") {
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141 out$tcn[out$tcn > 10] <- 9 + log10(out$tcn[out$tcn > 10])
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142 ii <- which(out$lcn > 5)
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143 if (length(ii) > 0) {
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144 out$lcn[ii] <- 5 + log10(out$lcn[ii])
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145 }
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146
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147 plot(c(0, length(jseg$cnlr)), c(0, max(out$tcn)),
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148 type = "n",
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149 ylab = "copy number (nv)", xaxt = "n"
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150 )
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151 abline(v = chrbdry, lwd = 0.25)
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152 segments(segstart, out$lcn, segend, out$lcn, lwd = 1.75, col = 2)
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153 segments(segstart, out$tcn, segend, out$tcn, lwd = 1.75, col = 1)
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154
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155 # Add legends for copy number plot (including CF legend)
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156 if (add.legend) {
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157 # CN legend on top left
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158 legend("topleft",
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159 legend = c("Total CN (TCN)", "Minor CN (LCN)"),
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160 col = c(1, 2),
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161 lwd = 1.75,
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162 bty = "n",
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163 cex = 0.7
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164 )
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165
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166 # CF legend on top right
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167 legend("topright",
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168 legend = c(
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169 "CF = 0 (normal)", "CF = 0.2 (low tumor)",
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170 "CF = 0.8 (high tumor)", "CF = 1.0 (pure tumor)"
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171 ),
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172 fill = c("white", "lightblue", "steelblue", "tan"),
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173 border = "black",
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174 bty = "o",
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175 box.col = "black",
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176 box.lwd = 1.5,
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177 cex = 0.65,
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178 title = "Cellular Fraction (CF)",
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179 bg = "white"
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180 )
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181 }
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182
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183 # CF bar (naive)
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184 plot(c(0, length(jseg$cnlr)), 0:1,
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185 type = "n", ylab = "",
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186 xaxt = "n", yaxt = "n"
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187 )
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188 mtext("cf-nv", side = 2, at = 0.5, line = 0.3, las = 2, cex = 0.75)
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189 cfcol <- cfpalette[round(10 * out$cf + 0.501)]
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190 rect(segstart, 0, segend, 1, col = cfcol, border = NA)
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191 }
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192
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193 # Plot 4: copy number (EM)
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194 if (plot.type == "em" | plot.type == "both") {
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195 out$tcn.em[out$tcn.em > 10] <- 9 + log10(out$tcn.em[out$tcn.em > 10])
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196 ii <- which(out$lcn.em > 5)
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197 if (length(ii) > 0) {
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198 out$lcn.em[ii] <- 5 + log10(out$lcn.em[ii])
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199 }
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200
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201 plot(c(0, length(jseg$cnlr)), c(0, max(out$tcn.em)),
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202 type = "n", ylab = "copy number (em)", xaxt = "n"
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203 )
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204 abline(v = chrbdry, lwd = 0.25)
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205 segments(segstart, out$lcn.em, segend, out$lcn.em, lwd = 1.75, col = 2)
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206 segments(segstart, out$tcn.em, segend, out$tcn.em, lwd = 1.75, col = 1)
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207
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208 # Add legends for EM copy number plot (including CF legend)
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209 if (add.legend) {
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210 # CN legend on top left
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211 legend("topleft",
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212 legend = c("Total CN (TCN)", "Minor CN (LCN)"),
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213 col = c(1, 2),
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214 lwd = 1.75,
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215 bty = "n",
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216 cex = 0.7
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217 )
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218
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219 # CF legend on top right
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220 legend("topright",
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221 legend = c(
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222 "CF = 0 (normal)", "CF = 0.2 (low tumor)",
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223 "CF = 0.8 (high tumor)", "CF = 1.0 (pure tumor)"
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224 ),
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225 fill = c("white", "lightblue", "steelblue", "tan"),
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226 border = "black",
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227 bty = "o",
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228 box.col = "black",
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229 box.lwd = 1.5,
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230 cex = 0.65,
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231 title = "Cellular Fraction (CF)",
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232 bg = "white"
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233 )
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234 }
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235
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236 # CF bar (EM)
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237 plot(c(0, length(jseg$cnlr)), 0:1,
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238 type = "n", ylab = "",
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239 xaxt = "n", yaxt = "n"
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240 )
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241 mtext("cf-em", side = 2, at = 0.5, line = 0.2, las = 2, cex = 0.75)
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242 cfcol <- cfpalette[round(10 * out$cf.em + 0.501)]
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243 rect(segstart, 0, segend, 1, col = cfcol, border = NA)
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244 }
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245
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246 # X-axis with chromosome labels
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247 chromlevels <- x$chromlevels
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248 if (is.null(chromlevels)) {
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249 chromlevels <- 1:length(nn)
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250 }
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251 axis(
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252 labels = chromlevels, side = 1,
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253 at = (nn + c(0, nn[-length(nn)])) / 2, cex = 0.65
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254 )
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255 mtext(side = 1, line = 1.75, "Chromosome", cex = 0.8)
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256
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257 # Sample name title
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258 if (!missing(sname)) {
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259 mtext(sname, side = 3, line = 0, outer = TRUE, cex = 0.8)
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260 }
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261
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262 par(def.par)
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263 }