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hdng / clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing
GNU General Public License v3.0
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Error in plot.clonal.models #32

Open fjgassner opened 4 years ago

fjgassner commented 4 years ago

I get the following output when running the plot.clonal.models pipeline:

Sample 1: Xvaf <-- Xvaf Sample 2: dup <-- dup Using monoclonal model Note: all VAFs were divided by 100 to convert from percentage to proportion. Generating non-parametric boostrap samples... Xvaf : Enumerating clonal architectures... Determining if cluster VAF is significantly positive... Exluding clusters whose VAF < min.cluster.vaf=0.01 Non-positive VAF clusters:
Xvaf : 1 clonal architecture model(s) found

dup : Enumerating clonal architectures... Determining if cluster VAF is significantly positive... Exluding clusters whose VAF < min.cluster.vaf=0.01 Non-positive VAF clusters:
dup : 1 clonal architecture model(s) found

Finding consensus models across samples... Found 1 consensus model(s) Generating consensus clonal evolution trees across samples... Found 1 consensus model(s) Scoring models... Pruning consensus clonal evolution trees.... Seeding aware pruning is: off Number of unique pruned consensus trees: 1 Error in polygon(xx, yy, col = fill.color[i], border = border.color[i], : invalid line type: must be length 2, 4, 6 or 8 In addition: Warning messages: 1: Removed 1 rows containing non-finite values (stat_summary). 2: Removed 1 rows containing missing values (geom_point). 3: Removed 1 rows containing non-finite values (stat_summary). 4: Removed 1 rows containing missing values (geom_point).

I use the following command:

plot.clonal.models(y, box.plot = TRUE, fancy.boxplot = TRUE, fancy.variant.boxplot.jitter.alpha = 1, fancy.variant.boxplot.jitter.center.color = "grey50", fancy.variant.boxplot.base_size = 12, fancy.variant.boxplot.plot.margin = 1, fancy.variant.boxplot.vaf.suffix = ".VAF", clone.shape = "bell", bell.event = FALSE, clone.time.step.scale = 1, bell.curve.step = 2, merged.tree.plot = TRUE, tree.node.label.split.character = NULL, tree.node.shape = "circle", tree.node.size = 30, tree.node.text.size = 0.5, merged.tree.node.size.scale = 1.25, merged.tree.node.text.size.scale = 2.5, merged.tree.cell.frac.ci = FALSE, merged.tree.clone.as.branch = TRUE, mtcab.branch.text.size = 2, mtcab.branch.width = 0.75, mtcab.node.size = 3, mtcab.node.label.size = 1, mtcab.node.text.size = 1.5, cell.plot = TRUE, num.cells = 100, cell.border.size = 0.25, cell.border.color = "black", clone.grouping = "horizontal", scale.monoclonal.cell.frac = TRUE, show.score = FALSE, cell.frac.ci = TRUE, disable.cell.frac = FALSE, out.dir = paste0("~/Documents/2019_09_06_Daniel/", filenames[i]), out.format = "pdf", overwrite.output = TRUE, width = 8, height = 4, panel.widths = c(3, 4, 2, 4, 2)) dev.off()

versions: clonEvol v0.99.11 R v. 3.6.1

fjgassner commented 4 years ago

For some reason, this error only occurs for samples with only one cluster.