plot_mean_exprs_heatmap: Plot mean expression heatmap
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

plot_mean_exprs_heatmap() plots a heatmap showing the mean expression of a gene in a monocle CellDataSet object.

plot_mean_exprs_heatmap(genes, cds, group, scale_method = NULL,
  cluster_groups = F, order_subgroups = F,
  cluster_groups_distance = "euclidean",
  cluster_groups_method = "complete", cluster_genes = F,
  cluster_genes_vector = NULL, cluster_genes_distance = "correlation",
  cluster_genes_method = "complete", color_scale = c("midnightblue",
  "gold", "grey50"), limits = NULL, square_tiles = T)

`genes`	a vector of gene name(s) to plot e.g. c("Actb", "Aldoa")
`cds`	a monocle CellDataSet object
`group`	column name in pData(cds) to group the bar plots by on the horizontal axis.
`scale_method`	scaling to be done for each gene; possible values are "z-score" and "rescale"; "z-score" scales the values to the z-scores; "rescale" scales the values to have a minimum of 0 and maximum of 1.
`cluster_groups`	logical; if groups should be clustered.
`order_subgroups`	logical; if subgroups should be ordered according to clustering of first subgroup. Subgroups can be specified in a string with separation by " - ".
`cluster_groups_distance`	distance measure used in clustering groups. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski" (defined in dist() function.)
`cluster_groups_method`	clustering method used for groups. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).
`cluster_genes`	logical; if genes should be clustered. If TRUE, genes with zero sd will be removed.
`cluster_genes_vector`	a vector specifying the order of genes. If NULL, genes will be clustered according to distance and method specified below.
`cluster_genes_distance`	distance measure used in clustering genes. Possible values are the same as cluster_groups_distance().
`cluster_genes_method`	clustering method used for genes. Possible values are the same as cluster_groups_method().
`color_scale`	color scale vector for heatmap of length 3 for low, high, and na values respectively; if null, limits of color scale will be determined by the squish() function
`limits`	limits of the color scale for the heatmap.
`square_tiles`	logical; if tiles should be made square