Description Usage Arguments Value Examples
View source: R/order_marker_matrix.R
order_marker_matrix() returns an expression matrix of marker genes ordered by cell group
1 2 3 4 5 6 | order_marker_matrix(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")
|
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. |
A matrix
1 | order_marker_matrix(dat, marker_genes = myMarkers, group_vector = "CellType")
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