chrisamiller
error generated from clonevol to fishplot
Hi Chrisamiller,
I came accorss an error like "Error in if (yst > 85 | yst < 15) { : missing value where TRUE/FALSE needed ", when importing clonevol results to fishplot. Would you help me to fix it.
Thanks Best Hao
Here is my code and input data.
code: library(clonevol) library(fishplot) data_demo = read.table('demo.tsv', header = T, sep = "\t") data_demo <- data_demo[order(data_demo$cluster),] vaf.col.names = grep('.vaf', colnames(data_demo), value=T) sample.names <- gsub('.vaf', '', vaf.col.names) clone.colors = NULL sample.groups <- c('Start','Time1','Time2','Time3','Time4','Time5') names(sample.groups) <- vaf.col.names
y = infer.clonal.models(variants = data_demo, cluster.col.name = 'cluster', ignore.clusters = NULL, vaf.col.names = vaf.col.names, ccf.col.names = NULL, sample.groups = sample.groups, cancer.initiation.model='monoclonal', subclonal.test = 'bootstrap', subclonal.test.model = 'non-parametric', num.boots = 1000, founding.cluster = 1, cluster.center = 'mean', clone.colors = clone.colors, min.cluster.vaf = 0.01, sum.p = 0.05, alpha = 0.05) #Mapping driver gene onto the evolutional tree y <- transfer.events.to.consensus.trees(y, data_demo[data_demo$is.driver,], cluster.col.name = 'cluster', event.col.name = 'gene')
f = generateFishplotInputs(results=y) fishes = createFishPlotObjects(f)
plot each of these with fishplot
pdf('fish.pdf', width=8, height=4) for (i in 1:length(fishes)){ fish = layoutClones(fishes[[i]]) fish = setCol(fish,f$clonevol.clone.colors) fishPlot(fish,shape="spline", title.btm="PatientID", cex.title=0.7, vlines=seq(1, length(vaf.col.names)), vlab=vaf.col.names, pad.left=0.5) } dev.off()
data-------demo.tsv
mutation_id cluster gene is.driver A11.vaf SP.vaf Xp2.vaf Xp3.vaf Xp5.vaf Xp6.vaf GPR4:FALSE 1 GPR4 FALSE 19.8 40 43.93 44.74 49.53 42.86 KRTAP24-1:FALSE 1 KRTAP24-1 FALSE 33.33 22.58 41.28 48.48 41.61 64.18 MLANA:FALSE 1 MLANA FALSE 23.26 87.5 81.48 100 100 100 PDP2:TRUE 1 PDP2 TRUE 37.5 27.27 87.23 100 98.86 100 PGAP1:FALSE 1 PGAP1 FALSE 0 44.44 58.82 64.29 24 62.5 SPIRE2:FALSE 1 SPIRE2 FALSE 26.15 48.68 76.14 100 97.2 97.06 ZNF860:FALSE 1 ZNF860 FALSE 25.71 19.05 67.69 100 100 100 DNAH14:FALSE 1 DNAH14 FALSE 41.51 52.27 53.16 56.06 53.93 66.67 HEATR2:FALSE 1 HEATR2 FALSE 41.67 31.71 65.32 80.46 69.08 67.65 NDUFA7:FALSE 1 NDUFA7 FALSE 39.19 57.14 64.44 100 100 100 NDUFV1:FALSE 1 NDUFV1 FALSE 18.6 24.14 43.48 46.97 30.57 24 NRG2:FALSE 1 NRG2 FALSE 30.3 53.49 56.14 59.55 53.21 56.14 PTPRF:FALSE 1 PTPRF FALSE 23.27 51.04 42.11 55.15 49.11 51.52 RELN:FALSE 1 RELN FALSE 22.16 40 38.53 49.53 48.27 50.72 TFR2:FALSE 1 TFR2 FALSE 24.23 49.57 43.18 54.9 51.9 50 ZNF658:FALSE 1 ZNF658 FALSE 44.44 36.36 50 51.72 63.46 62.5 CEP89:FALSE 1 CEP89 FALSE 20.25 40 51.28 49.4 40.77 45 DCAF4:FALSE 1 DCAF4 FALSE 36.13 50.51 84.82 100 100 98 DZIP1:FALSE 1 DZIP1 FALSE 19.12 34.78 33.33 62.5 51.91 43.24 EVA1B:FALSE 1 EVA1B FALSE 22.25 42.59 44.56 49.77 52.22 47.27 HACL1:FALSE 1 HACL1 FALSE 21.69 13.95 47.62 51.25 52.03 35.71 KBTBD7:FALSE 1 KBTBD7 FALSE 96.3 64 100 100 100 100 LRRK2:FALSE 1 LRRK2 FALSE 28.07 39.62 43.64 49.37 46.21 39.22 LTBP2:FALSE 1 LTBP2 FALSE 29.37 30.77 69.9 100 100 100 MUC6:FALSE 1 MUC6 FALSE 12.93 13.85 26.13 25.93 26.29 34.12 TRPM4:FALSE 1 TRPM4 FALSE 18.55 44.29 54.95 45.71 51.13 54.67 ZNF862:FALSE 1 ZNF862 FALSE 12.2 50.91 42.14 53.09 51.49 54.24 CEMIP:FALSE 1 CEMIP FALSE 31.58 31.03 75.31 100 100 100 CHSY1:FALSE 1 CHSY1 FALSE 27.27 24.49 83.61 100 98.63 100 FAM196B:FALSE 1 FAM196B FALSE 19.44 15.79 44.87 57.14 47.83 53.33 DPCR1:FALSE 2 DPCR1 FALSE 0 16.67 17.14 0 0 0 DPCR1:FALSE 2 DPCR1 FALSE 0 50 69.23 0 0 0 GSC:FALSE 2 GSC FALSE 0 35.29 0 0 0 0 LURAP1:FALSE 2 LURAP1 FALSE 23.29 63.64 51.69 59.26 47.88 60 SGTB:FALSE 2 SGTB FALSE 0 30 0 0 0 0 SIGLEC11:FALSE 2 SIGLEC11 FALSE 0 20 0 0 0 0 SYTL2:FALSE 2 SYTL2 FALSE 18.35 47.62 47.93 40.71 34.81 26.56 TBC1D22A:FALSE 2 TBC1D22A FALSE 0 44.74 0 0 0 0 ZNF587:FALSE 2 ZNF587 FALSE 0 55.17 0 0 0 0 ACOXL:FALSE 2 ACOXL FALSE 25.36 53.04 51.15 51.23 48.4 40.91 ALDH18A1:FALSE 2 ALDH18A1 FALSE 14.29 15.38 15.25 0 0 0 ASNS:FALSE 2 ASNS FALSE 20.49 60.78 55.15 50 48.03 45.45 FASN:TRUE 2 FASN TRUE 30 55.56 47.46 36.11 42.34 36.59 FSCB:FALSE 2 FSCB FALSE 0 100 100 90 0 100 FSCB:FALSE 2 FSCB FALSE 0 30 0 0 0 0 PRKAG2:FALSE 2 PRKAG2 FALSE 0 13.79 0 0 0 0 SNAPC4:FALSE 2 SNAPC4 FALSE 0 38.71 0 0 0 0 TCF20:FALSE 2 TCF20 FALSE 0 40 0 0 0 0 TNFRSF25:FALSE 2 TNFRSF25 FALSE 0 14.29 0 0 0 0 CNDP2:FALSE 2 CNDP2 FALSE 0 42.86 0 0 0 0 IQSEC3:FALSE 2 IQSEC3 FALSE 0 22.22 0 0 0 0 MAP4:FALSE 2 MAP4 FALSE 0 18.03 17.53 23.81 0 0 SIDT2:FALSE 2 SIDT2 FALSE 0 23.08 0 0 0 0 TPCN1:FALSE 2 TPCN1 FALSE 0 9.8 0 0 0 0 HCN4:FALSE 2 HCN4 FALSE 0 34.09 0 0 0 0 BAI3:FALSE 3 BAI3 FALSE 21.13 52.78 41.94 50 53.44 40.48 EXOC3L2:FALSE 3 EXOC3L2 FALSE 0 12.9 0 0 14.52 0 MUC16:FALSE 3 MUC16 FALSE 0 57.5 18.87 21.3 23.31 15.38 RSPH1:FALSE 3 RSPH1 FALSE 26.26 47.41 38.87 44.44 51.46 46.85 ZNF208:FALSE 3 ZNF208 FALSE 0 30 16.13 0 23.08 0 ZNF493:FALSE 3 ZNF493 FALSE 0 30.77 0 35 25.45 15.15 ZNF493:FALSE 3 ZNF493 FALSE 14.29 30.77 0 34.15 25 14.71 ZNF493:FALSE 3 ZNF493 FALSE 0 25 0 26.67 20.63 0 ARVCF:FALSE 3 ARVCF FALSE 0 9.3 0 0 0.58 0 CASKIN1:FALSE 3 CASKIN1 FALSE 13.95 75.56 61.54 65.38 61.84 66.67 FAM69B:FALSE 3 FAM69B FALSE 0 21.43 0 0 0 0 LEMD3:FALSE 3 LEMD3 FALSE 24.06 59.68 41.24 61.11 56.96 48.28 OBSCN:FALSE 3 OBSCN FALSE 23.63 58.08 42.62 53.08 45.92 50.27 PAF1:FALSE 3 PAF1 FALSE 0 50 29.09 48.15 34.25 52.38 SLC6A15:FALSE 3 SLC6A15 FALSE 25 66.67 31.58 42.11 44.44 70 TGDS:FALSE 3 TGDS FALSE 29.73 67.5 45.95 44.58 46.3 41.3 ANKZF1:FALSE 3 ANKZF1 FALSE 0 13.64 0 0 0 0 C17orf59:FALSE 3 C17orf59 FALSE 0 49.32 0 0 0 0 MYH9:TRUE 3 MYH9 TRUE 0 37.78 0 0 0 0 PCDHA10:FALSE 3 PCDHA10 FALSE 22.31 51.82 42.34 51.08 52.84 43.21 TAB2:FALSE 3 TAB2 FALSE 0 15 0 0 0 0 TYW1:FALSE 3 TYW1 FALSE 0 75 36.36 62.5 53.33 0 ZNF469:FALSE 3 ZNF469 FALSE 0 48.57 0 0 0 0 FN1:FALSE 3 FN1 FALSE 13.21 88.46 36.54 45 57.97 34.62 NEFM:FALSE 3 NEFM FALSE 0 40 0 0 0 0 PPP1R15B:FALSE 3 PPP1R15B FALSE 26.01 54.78 34.84 48.02 49.88 48.25 PRG4:FALSE 3 PRG4 FALSE 0 15.79 0 0 0 0 SIGLEC1:FALSE 3 SIGLEC1 FALSE 20.6 54.63 41.84 40.89 49.38 49.26 TMCC3:FALSE 3 TMCC3 FALSE 23.03 60.53 41.11 48.95 49.43 46.15 DPCR1:FALSE 4 DPCR1 FALSE 21.05 20 0 0 18.52 20 STRA6:FALSE 4 STRA6 FALSE 0 40 0 0 0 0 CDH5:TRUE 4 CDH5 TRUE 0 47.71 0 0 0 0 DNM2:FALSE 4 DNM2 FALSE 21.74 44.83 15.79 24.58 18.86 21.62 HSPA2:FALSE 4 HSPA2 FALSE 0 44.44 0 0 0 0 TET2:FALSE 4 TET2 FALSE 18.75 46.67 0 0 0 0 TPX2:FALSE 4 TPX2 FALSE 0 12.5 0 0 0 0 U2SURP:FALSE 4 U2SURP FALSE 0 17.5 0 0 0 0 ANKRD54:FALSE 4 ANKRD54 FALSE 0 15.79 0 0 0 0 ARHGEF10L:FALSE 4 ARHGEF10L FALSE 0 15.71 0 0 0 0 MAMDC4:FALSE 4 MAMDC4 FALSE 0 15 0 0 0 0 ST3GAL5:FALSE 4 ST3GAL5 FALSE 46.67 57.14 50 70.59 45.45 0 TSNAXIP1:FALSE 4 TSNAXIP1 FALSE 0 31.25 0 0 0 0 DYSF:FALSE 4 DYSF FALSE 0 14.29 0 0 0 0 OR52N4:FALSE 4 OR52N4 FALSE 0 34.09 0 0 0 0 SGMS2:FALSE 4 SGMS2 FALSE 34.21 46.67 0 0 0 0
