inferCNV clustering hierarchy troubleshoot

[dajunlee]

Hello, im trying to figure out cancer cell types from my dataset using inferCNV. There are few problems with analysing the data. 1) The result figure does not present hierarchies among clusters. 2) Nevetheless all cells from clusters should be divided to express different colors in each chromosome, my data does not.

I attach both my code and result png together. Please let me know how to solve this problem. Thanks

• code library(infercnv) infercnv_obj_full = infercnv::CreateInfercnvObject(raw_counts_matrix = GetAssayData(mlc, 'counts'), annotations_file = as.matrix(mlc@active.ident), gene_order_file = "./ref/data.broadinstitute.org_Trinity_CTAT_cnv_mouse_gencode.GRCm38.p6.vM25.basic.annotation.by_gene_name.infercnv_positions.txt", delim = '\t', ref_group_names = c('M1 macrophage', 'M2 macrophage'))

infercnv_obj_full_run = infercnv::run(infercnv_obj_full, out_dir = "./results/infercnv/20230906_2/", cutoff = 1, cluster_by_groups = T, HMM=F, denoise = T, plot_steps = F, sd_amplifier = 3, noise_logistic = T ) infercnv_obj_full_run_medianfiltered = infercnv::apply_median_filtering(infercnv_obj_full_run)

infercnv::plot_cnv(infercnv_obj_full_run_medianfiltered, out_dir = './results/infercnv/20230906_2', output_filename = 'infercnvR_nsclc_median_filtered2', x.range = 'auto', x.center = 1, title = 'inferCNV', color_safe_pal = F)

• result png

[zhangdae]

I have the same problem.A pic names infercnv_subcluster.png shows the subcluster of epithelial cells,but the number of subclusters in thee pic is not consistent with infercnv.png.I tried several days, can`t solve it.