plot_abundance: Plot clonotype abundance

In friedue/SCEdjvdj: Single-cell VDJ Tools for SCE objects

Description

Plot clonotype abundance

Usage

plot_abundance(
  SCE_in,
  clonotype_col = "cdr3_nt",
  cluster_col = NULL,
  calc_abundances = FALSE,
  plot_type = "bar",
  yaxis = "percent",
  plot_colors = NULL,
  plot_lvls = NULL,
  label_col = "cdr3",
  n_clonotypes = 5,
  color_col = NULL,
  label_aes = list(),
  facet_rows = 1,
  facet_scales = "free_x",
  ...
)

Arguments

SCE_in	Seurat object containing V(D)J data
clonotype_col	meta.data column containing clonotype IDs to use for calculating clonotype abundance
cluster_col	meta.data column containing cluster IDs to use for grouping cells when calculating clonotype abundance
calc_abundances	Default: FALSE. Set to TRUE if the clonotype abundances are not part of the SCE_in yet.
plot_type	Type of plot to create, can be 'bar' or 'line'
yaxis	Units to plot on the y-axis, either "frequency" or "percent"
plot_colors	Character vector containing colors for plotting
plot_lvls	Character vector containing levels for ordering
label_col	meta.data column containing labels to use for plot
n_clonotypes	Number of clonotypes to label
color_col	meta.data column to use for coloring bars
label_aes	Named list providing additional label aesthetics (color, size, etc.)
facet_rows	The number of facet rows. Use this argument if plot_type = 'bar'
facet_scales	If plot_type = 'bar', this argument passes a scales specification to facet_wrap, can be "fixed", "free", "free_x", or "free_y"
...	Additional arguments to pass to geom_line

Value

ggplot object

friedue/SCEdjvdj documentation built on April 21, 2021, 7:54 a.m.