Description Usage Arguments Examples
Comprehensive heatmap plot function with gene cluster and cell type labels.
1 2 | plot_heatmap_analysis(sorted_matrix, pseudo_time, cell_labels = NULL,
gene_cluster = NULL, heading = "HEATMAP", input_type = "hmm")
|
sorted_matrix |
This can be either the HMM matrix or the sorted gene selection matrix obtained from earlier functions. |
pseudo_time |
Pseudo development time |
cell_labels |
Defaults to NULL. The cell type labels. |
gene_cluster |
Defaults to NULL. It can be automatically caluclated with defualt gene cluster of 8. Or user can define the inferred gene cluster results using hierarchical clustering (get_gene_cluster) or by other means. Note that the input must match for the input matrix (ie gene / hmm) |
heading |
Plot title |
input_type |
"hmm" or "gene". Please specify type of sorted matrix input to the function. |
1 2 3 4 | selected_result <- gene_selection(full_exprs_matrix, redpath_pseudotime, dcor_result, mic_result, threshold = 0.5)
gene_state_result <- calc_all_hmm_diff_parallel(selected_result, cls_num = 2, threadnum = 4)
inferred_gene_cluster <- get_gene_cluster(sorted_matrix = gene_state_result, cls_num = 8)
heatmap_plot <- plot_heatmap_analysis(sorted_matrix = inferred_gene_cluster, redpath_pseudotime, cell_labels = NULL, gene_cluster = inferred_gene_cluster, input_type = "hmm")
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