heatmap_pseudobulk: Title

In Close-your-eyes/scexpr: Lots of helpers and wrappers to analyze scRNAseq data sets

Title

Description

Title

Usage

heatmap_pseudobulk(
  SO,
  meta.col = NULL,
  levels.calc = NULL,
  levels.plot = NULL,
  assay = c("RNA", "SCT"),
  features = NULL,
  order_features = F,
  normalization = "scale",
  topn.features = 10,
  topn.metric = c("logFC", "auc", "padj"),
  min.pct = 0.1,
  max.padj = 0.05,
  title = NULL,
  title.font.size = 14,
  font.family = "sans",
  y.font.size = 10,
  tile.borders = T,
  dotplot = F,
  plot.feature.breaks = T,
  plot.sec.axis = F,
  legend.position = "right",
  legend.direction = "vertical",
  legend.barheight = 8,
  legend.barwidth = 1,
  legend.text.size = 10,
  legend.title.text.size = 10,
  legend.title.fill = NULL,
  legend.title.size = NULL,
  legend.title.position = "top",
  legend.labels = c("min", "", "max"),
  feature.labels = NULL,
  feature.labels.nudge_x = -0.1,
  feature.labels.axis.width = 0.2,
  plot_hlines_between_groups = F,
  ...
)

Arguments

SO	Seurat object
meta.col	which column from meta.data of SO to use as x-axis; if NULL current Idents(SO) are used
levels.calc	which levels in meta.col to include in calculation; all levels if NULL; the order provided defines order on x-axis; level selection will affect scaling calculations
levels.plot	which levels in meta.col to include in platting; if NULL this equals to levels.calc; must be subset of levels.calc; the order provided defines order on x-axis; this will not affect scaling calculation but only select levels for plotting
assay	which assay to obtain expression values from
features	optionally choose which features to plot (supervised)
order_features	when features are provided should they be ordered automatrically to generate a pretty heatmap; not relevant when is.null(features)
normalization	how to scale expression values; may be "scale" to use base::scale and transform average expression value to a standardized normal distribution or may be a numeric vector of length 2 for scaling each feature from min (first value) to max (second value); in the latter case c(-1,1) is most meaningful
topn.features	if no features are selected, this will select how many features to plot per level in meta.col; selection is done based on the metric selected in topn.metric; respective features with greatest difference between meta.col levels are selected (best DE features so to say)
topn.metric	which differential expression metric to apply for feature selection
min.pct	filter features across levels in meta.col for a minimal fraction of expressing cells; 0.1 stands for min 10 % expressing cells
max.padj	filter features across levels in meta.col for a significance level of differential expression (one level vs. all others)
title	which title to add to plot; if NULL no title is plotted
title.font.size	font size of title
font.family	which font type (family) to use for plotting, e.g. mono or sans
y.font.size	font size of features names on y-axis
tile.borders	plot black tile border (TRUE) or not (FALSE); better set to FALSE for may features and optionally set to TRUE for few features only
dotplot	plot heatmap as a dotplot which will also reveal the fraction of expressing cells by dot sizes
plot_hlines_between_groups

Close-your-eyes/scexpr documentation built on April 21, 2023, 10:27 a.m.