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!