Heatmap PNG still blank after setting bitmapType to Xlib on Ubuntu 22.04

[wudustan]

Hi,

I have installed all the necessary prerequisites and set the necessary options in R but I still get a blank .png file.

library(infercnv)

cxj076.icnv <- infercnv::CreateInfercnvObject(raw_counts_matrix = merged.counts,
                                    annotations_file="infercnv/cxj076/cxj076_types_map.txt",
                                    gene_order_file="infercnv/cxj076/cxj076_gene_map.txt",
                                    ref_group_names = "Normal")

options(scipen = 100)
options(bitmapType="Xlib")
cxj076.icnv <- infercnv::run(cxj076.icnv,
                             cutoff = 0.1,
                             out_dir = "infercnv/cxj076_out/", 
                             analysis_mode = "subclusters",
                             num_threads = 16,
                             k_obs_groups = 3,
                             cluster_by_groups = FALSE,
                             plot_steps = FALSE, 
                             no_prelim_plot = TRUE, 
                             denoise = TRUE, 
                             HMM = FALSE,
                             png_res = 300)

The plotting function returns no error output and the sizes of the plot data are below:

Observation data size: Cells= 33779 Genes= 8151 Reference data size: Cells= 24607 Genes= 8151

Can anyone advise what else to try? I suppose I probably am running into limitations of the rasterisation? Alternatively, does anyone have some nice code for visualising the data outside of the infercnv package?

[GeorgescuC]

Hi @wudustan ,

Besides setting the bitmapType, if you are running this on a server, have you set X11 forwarding? You can find instructions on the wiki.

Alternatively, you can also try using the NGCHM viewer to visualize the results in .

Regards, Christophe.