view.aspects | R Documentation |
Internal function to visualize aspects of transcriptional heterogeneity as a heatmap.
view.aspects(
mat,
row.clustering = NA,
cell.clustering = NA,
zlim = c(-1, 1) * quantile(mat, p = 0.95),
row.cols = NULL,
col.cols = NULL,
cols = colorRampPalette(c("darkgreen", "white", "darkorange"), space = "Lab")(1024),
show.row.var.colors = TRUE,
top = Inf,
...
)
mat |
Numeric matrix |
row.clustering |
Row dendrogram (default=NA) |
cell.clustering |
Column dendrogram (default=NA) |
zlim |
numeric Range of the normalized gene expression levels, inputted as a list: c(lower_bound, upper_bound) (default=c(-1, 1)*quantile(mat, p = 0.95)). Values outside this range will be Winsorized. Useful for increasing the contrast of the heatmap visualizations. Default, set to the 5th and 95th percentiles. |
row.cols |
Matrix of row colors (default=NULL) |
col.cols |
Matrix of column colors (default=NULL). Useful for visualizing cell annotations such as batch labels. |
cols |
Heatmap colors (default=colorRampPalette(c("darkgreen", "white", "darkorange"), space = "Lab")(1024)) |
show.row.var.colors |
boolean Whether to show row variance as a color track (default=TRUE) |
top |
integer Restrict output to the top n aspects of heterogeneity (default=Inf) |
... |
additional arguments for heatmap plotting |
A heatmap
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.