feature_plot: Plot features of single cell transcriptomes on a dimension...

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

Plot features of single cell transcriptomes on a dimension reduction map

Description

Plot features of single cell transcriptomes on a dimension reduction map

Usage

feature_plot(
  SO,
  features,
  assay = c("RNA", "SCT"),
  dims = c(1, 2),
  cells = NULL,
  downsample = 1,
  pt.size = 1,
  pt.size.expr.factor = 1,
  order = T,
  order.abs = T,
  shuffle = T,
  order.rev = F,
  min.q.cutoff = 0,
  max.q.cutoff = 1,
  reduction = "umap",
  split.by = NULL,
  split.by.scales = "fixed",
  shape.by = NULL,
  combine = T,
  ncol.combine = NULL,
  nrow.combine = NULL,
  nrow.inner = NULL,
  ncol.inner = NULL,
  feature.aliases = NULL,
  binary = F,
  title = NULL,
  title.font.size = 14,
  cutoff.feature = NULL,
  cutoff.expression = 0,
  exclusion.feature = NULL,
  legend.position = "right",
  legend.title.text.size = 14,
  legend.text.size = 10,
  legend.barheight = 3,
  legend.barwidth = 0.5,
  legend.nrow = NULL,
  legend.ncol = NULL,
  legend.key.size = 0.3,
  legend.shape.size = 3,
  legend.col.size = 3,
  hide.shape.legend = F,
  font.family = "sans",
  col.pal.c = "spectral",
  col.pal.d = "custom",
  col.excluded.cells = "grey95",
  col.non.expresser = "grey85",
  col.expresser = "tomato2",
  col.pal.rev = F,
  theme = ggplot2::theme_bw(),
  plot.axis.labels = F,
  plot.panel.grid = F,
  plot.freq.title = NULL,
  plot.freq = NULL,
  plot.legend.title = F,
  plot.title = T,
  order.discrete = T,
  freq.position = c(-Inf, Inf),
  freq.font.size = 4,
  plot.cutoff.feature.inset = F,
  inset.position = c(0.75, 0.1),
  inset.size = c(0.15, 0.15),
  strip.font.size = 14,
  strip.selection = NA,
  plot.labels = NULL,
  label.size = 12,
  na.rm = F,
  inf.rm = F,
  bury_NA = T,
  trajectory.slot = NULL,
  trajectory.color = "grey30",
  trajectory.size = 0.75,
  trajectory.linetype = "solid",
  contour_feature = NULL,
  col.pal.contour = "custom",
  contour_args = list(contour_var = "ndensity", breaks = 0.3, linewidth = 1),
  plot.expr.freq.by.contour.group = F,
  use_ggnewscale_for_contour_colors = T,
  expand_limits = list(),
  ...
)

Arguments

SO	one or more Seurat object(s)
features	vector of features to plot (genes or column names in meta data)
assay	which assay to get expression data from
dims	which dimensions of the selected dimension reduction to plot
cells	a vector of cell names to include (not selected ones are plotted with color col.excluded.cells)
downsample	downsample the number of cells (intended to speed up test plottings)
pt.size	dot size per cells
pt.size.expr.factor	factor of increased dot size for expressing cells
order	for meta.col: remains T if var is continuous but becomes F if var is integer (~probably discrete)
order.abs	do use absolute values for ordering (any value away from zero (+/) is treated equally)
shuffle	do shuffle if order if FALSE; allows to define a definite order for plotting if set to to F
order.rev	reverse the ordering to have lowest values on top (or zeros if order.abs = T)
min.q.cutoff	decimal number (> 1, < 0) of lower quantile limit where to cut the color scale, intended to squish extremes
max.q.cutoff	decimal number (> 1, < 0) of upper quantile limit where to cut the color scale, intended to squish extremes
reduction	which reduction to use for plotting
split.by	column in meta data to use to split plots
shape.by	column in meta data to shape dots (cells) b<
combine	combine multiple features to one plot (TRUE) or return a list with one entry per feature (FALSE)
ncol.combine	number of columns in combined graphic (feature combined)
nrow.combine	number of rows in combined graphic (feature combined)
nrow.inner	number of plots per row within one feature (originating from multiple SO and/or split.by)
ncol.inner	number of plots per column within one feature (originating from multiple SO and/or split.by)
feature.aliases	vector aliases for features; e.g. c("FAIM3" = "FCMR", "MS4A1" = "CD20")
title	force title for the plot instead of feature name which is the default
title.font.size	font size of the title
cutoff.feature	select a feature for cells to consider in plotting
cutoff.expression	select the cutoff feature expression levels for filtering
legend.position	values between 0 and -1
trajectory.slot	name of Misc slot that contains information on how to plot a trajectory
expand_limits

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