sample_heatmap_plot: Heatmaps of gene expression for individual samples. THIS...

In AllenInstitute/L5_VEN:

Heatmaps of gene expression for individual samples. THIS FUNCTION IS NOW IN library(scrattch.vis)

Description

Heatmaps of gene expression for individual samples. THIS FUNCTION IS NOW IN library(scrattch.vis)

Usage

sample_heatmap_plot(data_source, genes = c("Hspa8", "Snap25", "Gad2",
  "Vip"), group_by = "cluster", groups = 1:10, top_labels = "layer",
  sample_n = 0, scale_mode = "scale.log", showall = F,
  autorange = "auto", minrange = 0, maxrange = 10, pfontsize = 14,
  expand = F, rotatelabels = F, showlines = F, showids = T)

Arguments

genes	A character vector containing gene symbols to be plotted.
data	A data frame containing gene expression values. The first column should be sample_name
anno	Sample annotations. The first column should be sample_name, and each annotation should have \_id, \_label, and \_color columns
grouping	A character vector specifying the desc base that should be used to group cells
group_order	Optional: Explicit specification of group order by supplying a vector of group_ids.
log_scale	Logical , determines if data is log scaled before plotting. Default = FALSE.
normalize_rows	Logical, determines if heatmaps will be normalized for each gene. Default = FALSE.
font_size	numeric object, the font size (in pts) used to make the plot.
label_height	numeric object, Percent of the plot height that should be used for the labels (0 to 100). Default is 25.
label_type	Label shape, "angle" or "square"
max_width	numeric object, percent of plot width that should be used for maximum expression values (0 to 100). Default is 10.
return_type	What values to return - can be "plot", "data", or "both". Default is "plot".

Value

a ggplot2 plot object

AllenInstitute/L5_VEN documentation built on July 31, 2022, 6:32 p.m.