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farrellja / URD

URD - Reconstruction of Branching Developmental Trajectories
GNU General Public License v3.0
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Error in visit.data[cells.in.tip, ] : incorrect number of dimensions #83

Open zhang929821416 opened 1 year ago

zhang929821416 commented 1 year ago

Hi Team URD! thank you for the development of such a nice package! I got the following error when I run buildTree: tree <- buildTree(object = object_adding_walks, pseudotime = "pseudotime", divergence.method = "preference", tips.use = tip.to.walk, weighted.fusion = TRUE, use.only.original.tips = TRUE, cells.per.pseudotime.bin = 80, bins.per.pseudotime.window = 10, minimum.visits = 1, visit.threshold = 0.7, p.thresh = 0.025, save.breakpoint.plots = TRUE, dendro.node.size = 100, dendro.cell.jitter = 0.15, dendro.cell.dist.to.tree = 0.01, min.cells.per.segment = 10, min.pseudotime.per.segment = 0.01, verbose = TRUE) [1] "Calculating divergence between 1 and 2 (Pseudotime 0 to 0.546)" Difference between 1 and 2 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 1 and 3 (Pseudotime 0 to 0.546)" Difference between 1 and 3 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 1 and 4 (Pseudotime 0 to 0.546)" Difference between 1 and 4 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 1 and 5 (Pseudotime 0 to 0.546)" Difference between 1 and 5 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 1 and 6 (Pseudotime 0 to 0.546)" Difference between 1 and 6 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 1 and 7 (Pseudotime 0 to 0.546)" Difference between 1 and 7 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 1 and 8 (Pseudotime 0 to 0.546)" Difference between 1 and 8 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 2 and 3 (Pseudotime 0 to 0.546)" Difference between 2 and 3 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 2 and 4 (Pseudotime 0 to 0.546)" Difference between 2 and 4 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 2 and 5 (Pseudotime 0 to 0.546)" Difference between 2 and 5 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 2 and 6 (Pseudotime 0 to 0.546)" Difference between 2 and 6 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 2 and 7 (Pseudotime 0 to 0.546)" Difference between 2 and 7 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 2 and 8 (Pseudotime 0 to 0.546)" Difference between 2 and 8 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 3 and 4 (Pseudotime 0 to 0.546)" Difference between 3 and 4 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 3 and 5 (Pseudotime 0 to 0.546)" Difference between 3 and 5 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 3 and 6 (Pseudotime 0 to 0.546)" Difference between 3 and 6 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 3 and 7 (Pseudotime 0 to 0.546)" Difference between 3 and 7 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 3 and 8 (Pseudotime 0 to 0.546)" Difference between 3 and 8 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 4 and 5 (Pseudotime 0 to 0.546)" Difference between 4 and 5 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 4 and 6 (Pseudotime 0 to 0.546)" Difference between 4 and 6 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 4 and 7 (Pseudotime 0 to 0.546)" Difference between 4 and 7 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 4 and 8 (Pseudotime 0 to 0.546)" Difference between 4 and 8 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 5 and 6 (Pseudotime 0 to 0.546)" Difference between 5 and 6 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 5 and 7 (Pseudotime 0 to 0.546)" Difference between 5 and 7 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 5 and 8 (Pseudotime 0 to 0.546)" Difference between 5 and 8 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 6 and 7 (Pseudotime 0 to 0.546)" Difference between 6 and 7 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 6 and 8 (Pseudotime 0 to 0.546)" Difference between 6 and 8 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 7 and 8 (Pseudotime 0 to 0.546)" Difference between 7 and 8 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 1 and 2 at pseudotime 0.546 to create segment 9" [1] "Calculating divergence between 3 and 9 (Pseudotime 0 to 0.546)" Difference between 3 and 9 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 4 and 9 (Pseudotime 0 to 0.546)" Difference between 4 and 9 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 5 and 9 (Pseudotime 0 to 0.546)" Difference between 5 and 9 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 6 and 9 (Pseudotime 0 to 0.546)" Difference between 6 and 9 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 7 and 9 (Pseudotime 0 to 0.546)" Difference between 7 and 9 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 8 and 9 (Pseudotime 0 to 0.546)" Difference between 8 and 9 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 3 and 4 at pseudotime 0.546 to create segment 10" [1] "Calculating divergence between 5 and 10 (Pseudotime 0 to 0.546)" Difference between 5 and 10 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 6 and 10 (Pseudotime 0 to 0.546)" Difference between 6 and 10 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 7 and 10 (Pseudotime 0 to 0.546)" Difference between 7 and 10 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 8 and 10 (Pseudotime 0 to 0.546)" Difference between 8 and 10 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 9 and 10 (Pseudotime 0 to 0.546)" Difference between 9 and 10 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 5 and 6 at pseudotime 0.546 to create segment 11" [1] "Calculating divergence between 7 and 11 (Pseudotime 0 to 0.546)" Difference between 7 and 11 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 8 and 11 (Pseudotime 0 to 0.546)" Difference between 8 and 11 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 9 and 11 (Pseudotime 0 to 0.546)" Difference between 9 and 11 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 10 and 11 (Pseudotime 0 to 0.546)" Difference between 10 and 11 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 7 and 8 at pseudotime 0.546 to create segment 12" [1] "Calculating divergence between 9 and 12 (Pseudotime 0 to 0.546)" Difference between 9 and 12 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 10 and 12 (Pseudotime 0 to 0.546)" Difference between 10 and 12 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 11 and 12 (Pseudotime 0 to 0.546)" Difference between 11 and 12 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 9 and 10 at pseudotime 0.546 to create segment 13" [1] "Calculating divergence between 11 and 13 (Pseudotime 0 to 0.546)" Difference between 11 and 13 always FALSE -- setting breakpoint to end. [1] "Calculating divergence between 12 and 13 (Pseudotime 0 to 0.546)" Difference between 12 and 13 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 11 and 12 at pseudotime 0.546 to create segment 14" [1] "Calculating divergence between 13 and 14 (Pseudotime 0 to 0.546)" Difference between 13 and 14 always FALSE -- setting breakpoint to end. [1] "Saving breakpoint decision plot." [1] "Joining segments 13 and 14 at pseudotime 0.546 to create segment 15" [1] "Assigning cells to segments." [1] "Collapsing short segments." [1] "Removing singleton segments." [1] "Reassigning cells to segments." Error in visit.data[cells.in.tip, ] : incorrect number of dimensions In addition: There were 50 or more warnings (use warnings() to see the first 50)

It would be great if anyone has ideas about how to fix this error. Thanks. @farrellja @zouter @maximilianh