plot_marker_heatmap: Plot heatmap of marker genes ordered by cell group
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

plot_marker_heatmap() plots a heatmap with genes ordered by cell group.

plot_marker_heatmap(cds, marker_genes, group_vector, scale = T,
  cluster_rows = T, cluster_cols = T,
  clustering_distance_rows = "euclidean",
  clustering_method_rows = "complete",
  clustering_distance_cols = "euclidean",
  clustering_method_cols = "complete", column_annotation,
  limits = c(-2, 2), show_rownames = T, show_colnames = F)

`cds`	CellDataSet object
`marker_genes`	dataframe containing 2 columns: (1) gene symbol (2) cell group e.g. CellType
`group_vector`	a vector classifying cells e.g. genotype or condition
`scale`	"rows" or "cols" or "none"; indicates whether values should be centered and scaled in the row direction or the column direction or none.
`cluster_rows`	logical; if rows should be clustered
`cluster_cols`	logical; if columns should be clustered
`clustering_distance_rows`	distance measure used in clustering rows. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski" (defined in dist() function.)
`clustering_method_rows`	clustering method used for rows. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).
`clustering_distance_cols`	distance measure used in clustering columns. Possible values are the same as clustering_distance_rows.
`clustering_method_cols`	clustering method used for columns. Accepts the same values as clustering_method_rows.
`column_annotation`	column names in pData(cds) for annotating columns of heatmap
`limits`	limits of color scale of heatmap
`show_rownames`	logical; if rownames of heatmap should be displayed
`show_colnames`	logical; if colnames of heatmap should be displayed
`annotation_colors`	list for specifying annotation_row and annotation_col track colors manually as specified in pheatmap. It is possible to define the colors for only some of the features.