heatmap_gene_clusters: Draw heatmaps of gene clusters from output of...

In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data

Description

Draw heatmaps of gene clusters from output of 'smooth_and_cluster_genes'.

Usage

heatmap_gene_clusters(dge, results_path, cluster_mod, smoothers,
  gap_size = NULL, genes_use = NULL, genes_to_label = NULL)

Arguments

dge	Seurat object with raw data and pseudotime metadata used to train smoothers. If metadata 'simple_branch' is present, function is hardwired to look for "mTEC", "cTEC", "branchpoint", and "progenitor" and make a heatmap similar to figure 2 in http://dx.doi.org/10.1101/122531.
results_path	Where to save plots and files.
cluster_mod	K-means output with cluster labels for the genes in 'smoothers' and also with cluster centers.
smoothers	List of regression models for the genes in 'cluster_mod' and 'gene_stats'.
gap_size	White bars separating clusters are formed by adding fake genes. gap_size is how many fake genes per bar.
genes_use	Gene names or anything in 'AvailableData(dge)'.
genes_to_label	Subset of 'genes_use' to write tick labels for.

maehrlab/thymusatlastools documentation built on May 28, 2019, 2:32 a.m.