Comments (3)
Thanks for your efforts to develop this package @koustav-pal
We've replicated this issue (@kuguit and I) when plotting trans-chromosomal contacts between chromosomes of different sizes (x-axes chromosome was smaller than y-axes). The y_coords therefore did not match the axes limits defined by x_coords or the maximum length of the shorter chromosome.
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'end': subscript contains out-of-bounds indices
I've found the bug causing this and have a working solution which allows:
- different co-ordinate inputs for each chromosome
- plotting asymmetric matrices which axes of different sizes
- inverting the matrix to (optionally) allow plotting the larger chromosome on the x-axis from the same "brick" file
I've tested this solution by modifying the function code and running "source" on this R script to import the update version. I'll submit a pull request with recommended changes.
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I think this solution will resolve issue #17 as well.
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I've added these as 2 separate PRs as #25 directly addresses this issue while #26 significantly changes the codebase to allow transpose matrices in the lower triangle to be plotted.
- different co-ordinate inputs for each chromosome (see PR #25)
- plotting asymmetric matrices which axes of different sizes (see PR #25)
- inverting the matrix to (optionally) allow plotting the larger chromosome on the x-axis from the same "brick" file (see PR #26)
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Related Issues (19)
- Bug when creating a new brick with the same path/name of a previous brick HOT 1
- Show me a Heatmap HOT 1
- problem loading mcool file HOT 10
- Integrate direct access to .hic files HOT 1
- Norm.factor not found HOT 3
- Implement Brick container for parallelization HOT 1
- Need help to read in the mcool file converted by hicexplorer HOT 1
- Vignette examples cannot be followed HOT 2
- Add support for HiCExplorer files
- Is it possible to separate Hi-C signal into weights and observed contacts
- any suggestion on how to generate aggregate submatrix plot HOT 2
- If x_axis is false Brick_vizart_plot_heatmap does not plot y_axis
- Pearson correlation matrix
- Package failing on Bioconductor HOT 3
- Error running Create_many_Bricks with H5 HOT 1
- Plotting more than one chromosome at once HOT 2
- error: invalid 'times' argument
- Is "chrs" removed from Create_many_Bricks_from_mcool or Brick_load_data_from_mcool?
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