group_heatmap_plot: Heatmap plots of group summary statistics. THIS FUNCTION IS...

In AllenInstitute/L5_VEN:

Heatmap plots of group summary statistics. THIS FUNCTION IS NOW IN library(scrattch.vis)

Description

Heatmap plots of group summary statistics. THIS FUNCTION IS NOW IN library(scrattch.vis)

Usage

group_heatmap_plot(genes = c("Hspa8", "Snap25", "Gad2", "Vip"),
  clusters = 1:10, group_by = "final", calculation = "mean",
  data_source = "internal", normalize_rows = FALSE, logscale = T,
  fontsize = 7, labelheight = 25, max_width = 10, showcounts = T,
  rotatecounts = F, maxval = "auto", colorset = c("darkblue",
  "dodgerblue", "gray80", "orange", "orangered"))

Arguments

genes	A character vector containing gene symbols to be plotted.
normalize_rows	Logical, whether or not to rescale data within each row of the plot. Default = FALSE.
max_width	numeric object, percent of plot width that should be used for maximum expression values (0 to 100). Default is 10.
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.
stat	The statistic to apply to each group. Options are: "median" "mean" "tmean" (25% trimmed mean) "nzmean" (mean of non-zero values) "nzmedian" (median of non-zero values) "prop_gt0" (proportion of samples > 0) "prop_gt1" (proportion of samples > 1) "min" "max"
log_scale	Logical , determines if data is log scaled before plotting. 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.
show_counts	Logical, whether or not to display sample counts at the top of labels. Default = TRUE.
rotate_counts	Logical, whether or not to rotate sample counts by 90 degrees. Default = FALSE.
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.