plot_hmm_full: Plot function for HMM & gene expression changes

In tinglab/redPATH: Reconstructing the pseudo development time of cell lineages in single cell RNA-Seq data and applications in cancer.

Description

Various versions of plots are available here to visualize the most significant gene expression change from dCor and MIC.

Usage

plot_hmm_full(sorted_exprs_val, pseudotime, sorted_hmm_results = NULL,
  color_label = NULL, num_plots = 10)

Arguments

sorted_exprs_val	The gene expression input obtained from gene_selection. The ranked and sorted gene_expression matrix.
pseudotime	Pseudo development time
sorted_hmm_results	Defaults to NULL. This is the inferred HMM matrix obtained from calc_all_hmm_diff_parallel.
color_label	Defaults to NULL. The cell type labels.
num_plots	Number of plots desired, ranking from the most significant.

Examples

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)
hmm_plots <- plot_hmm_full(selected_result, redpath_pseudotime, gene_state_result, cell_type_label, num_plots = 10)
require(scater)
multiplot(plotlist = hmm_plots, layout = matrix(c(1:10), 5, 2)) # For a total number of 10 plots

tinglab/redPATH documentation built on May 31, 2019, 10:37 a.m.