I am plotting a large number of cells around 30,000 because of this I believe I got blank plots. I was reading a previously closed issue where you suggested using plot_chr_scale=T . When I did this I got a filled in plot but it was not longer plotted by seurat clusters, just one big heatmap. I also tried useRaster = T but that resulted in blank plots. Do you have on what I need to do to get a heatmap plotted by seurat clusters like I normally get with smaller datasets? This is my run code for the one big heatmap.
infercnv_obj1 = infercnv::run(infercnv_obj,
cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
out_dir=out_dir,
cluster_by_groups=T, analysis_mode="samples",
tumor_subcluster_partition_method = "leiden",
plot_steps=T, plot_probabilities=T, no_prelim_plot=F, no_plot=F,
denoise=T, noise_filter=0.12,
HMM=F, HMM_type='i3',
num_threads=10,
plot_chr_scale=T)
Hi @GeorgescuC ,
I am plotting a large number of cells around 30,000 because of this I believe I got blank plots. I was reading a previously closed issue where you suggested using plot_chr_scale=T . When I did this I got a filled in plot but it was not longer plotted by seurat clusters, just one big heatmap. I also tried useRaster = T but that resulted in blank plots. Do you have on what I need to do to get a heatmap plotted by seurat clusters like I normally get with smaller datasets? This is my run code for the one big heatmap.
infercnv_obj1 = infercnv::run(infercnv_obj, cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics out_dir=out_dir, cluster_by_groups=T, analysis_mode="samples", tumor_subcluster_partition_method = "leiden", plot_steps=T, plot_probabilities=T, no_prelim_plot=F, no_plot=F, denoise=T, noise_filter=0.12, HMM=F, HMM_type='i3', num_threads=10, plot_chr_scale=T)
Thank you so much for all of your help!