Section of inferCNV heatmap blacked out

[julie-jch]

Hello Team,

I'm encountering a strange issue. I am running inferCNV on some data, and every time I attempt to generate a plot, the bottom section of the plot is blacked out.

The data has ~55000 cells I am running it on a Linux server infercnv version: 1.12.0

code used to generate plot

infercnv_obj = infercnv::run(infercnv_obj,
                             cutoff=0.1, 
                             out_dir=out_dir, 
                             cluster_by_groups=TRUE, 
                             denoise=TRUE,
                             HMM=FALSE,
                             no_plot=FALSE,
                             output_format="pdf",
                             num_threads=18)

Additional Information: If I run plot per group, all images are generated well.

 infercnv::plot_per_group(infercnv_obj,
                          out_dir=out_dir,
                          output_format="pdf")

When I call the plot_cnv() and try to generate the heatmap this way, I get the same issue.

plot_cnv(infercnv_obj,
         out_dir=out_dir,
         obs_title="Observations (Cells)",
         ref_title="References (Cells)",
         cluster_by_groups=TRUE,
         x.center=1,
         x.range="auto",
         hclust_method='ward.D',
         color_safe_pal=FALSE,
         output_filename="infercnv_heatmap",
         output_format="pdf",
         dynamic_resize=0
         )