Error in plot.new() : figure margins too large

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Christopher Zou

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Apr 3, 2023, 4:06:36 AM4/3/23
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Hi all -

I'm running inferCNV on a sample of some 16,000 genes, with 25,000 features. I'm getting an error that is as follows:

```Error in plot.new(): figure margins too large```

I am seeing this warning: 

plot_cnv(): auto thresholding at: (0.879758 , 1.122283)
WARN [2023-04-02 23:56:59] Requested PNG output height too big at the current resolution, using the max height instead. (cairo seems to have a size limit of 32767 (2^15-1) pixels per dimension and 49151 (2^15+2^14-1)pixels for the sum of dimensions)

Folks at UCSF suggested that I decrease the resolution of the clustering, but I'm not sure how far I can push it. I do seem to still see a lot of clusters with only 1 or 2 cells. Here are my running parameters at the moment:

infercnv_obj = infercnv::run(infercnv_obj,
                             cutoff=0.1,  # use 1 for smart-seq, 0.1 for 10x-genomics
                             out_dir="output_dir_cleaned_integrate_downsampled8",  # dir is auto-created for storing outputs
                             cluster_by_groups=TRUE,   # cluster
                             denoise=TRUE,
                             HMM=TRUE,
                             num_threads = 10,
                             tumor_subcluster_partition_method="leiden",
                             tumor_subcluster_pval=0.1,
                             leiden_resolution=0.025
)

Would love any pointers! Thank you!
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