Fix division-by-zero in filter.points & as.vector regression in multi-traits#153
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lyangfan wants to merge 2 commits intoYinLiLin:masterfrom
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Fix division-by-zero in filter.points & as.vector regression in multi-traits#153lyangfan wants to merge 2 commits intoYinLiLin:masterfrom
lyangfan wants to merge 2 commits intoYinLiLin:masterfrom
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In the density plot, filter.points is called with a constant y value (per-chromosome band position), making y_max - y_min = 0. This causes 0/0 = NaN, collapsing all keys to NaN and making duplicated() keep only the first point per group. The result is severe point loss in density plots. Fix: check for zero range before division; assign 0L to scaled values when range is 0, preserving correct point filtering behavior.
as.vector() on a multi-column data.frame does not flatten it to a numeric vector, causing min() to fail with "invalid type (list)". Use unlist() first. Bug existed since upstream (2023-06-28). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Summary
1. Fix division-by-zero in
filter.pointscausing density plot point lossfilter.pointsis called with constant y values in density rendering. Wheny_range == 0,(y - y_min) / (y_max - y_min)produces0/0 = NaN. R'sduplicated()treats the firstNaNas unique and all subsequent as duplicates, collapsing the entire density bar to a single pixel.Reproduce:
2. Fix
as.vectorregression in multi-traits modeThe optimization commit (23905fc) removed
Pmap <- as.matrix(Pmap)to keep Pmap as data.frame for performance. However,as.vector(Pmap[,3:(R+2)])in the multi-traits section relies on Pmap being a matrix —as.vector()on a data.frame (which is a list) returns it unchanged. Subsequentmin_no_na(pvalue)→min(list, na.rm=TRUE)crashes.Reproduce:
🤖 Generated with Claude Code