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Plot clonotype abundance

Source: R/calc-abundance.R
plot_clonal_abundance.Rd

Plot clonotype abundance

Usage

plot_clonal_abundance(
  input,
  cluster_col = NULL,
  clonotype_col = "clonotype_id",
  method = "bar",
  units = "percent",
  plot_colors = NULL,
  plot_lvls = names(plot_colors),
  n_clones = NULL,
  label_aes = list(),
  panel_nrow = NULL,
  panel_scales = "free_x",
  ...
)

Arguments

input

Single cell object or data.frame containing V(D)J data. If a data.frame is provided, the cell barcodes should be stored as row names.

cluster_col

meta.data column containing cluster IDs to use for grouping cells when calculating clonotype abundance. Clonotypes will be plotted separately for each cluster.

clonotype_col

meta.data column containing clonotype IDs to use for calculating clonotype abundance

method

Method to use for plotting, 'bar' will generate a bargraph, 'line' will generate a rank-abundance plot.

units

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

n_clones

Number of top clonotypes to plot (default is 10). If method is set to 'line', this will specify the number of clonotypes to label (default is 3).

label_aes

Named list providing additional aesthetics (color, size, etc.) for clonotype labels when creating line graph

panel_nrow

The number of rows to use for arranging plot panels, use this when separate bar graphs are created for each cell cluster

panel_scales

Should scales for plot panels be fixed or free. This passes a scales specification to ggplot2::facet_wrap, can be 'fixed', 'free', 'free_x', or 'free_y'. 'fixed' will cause panels to share the same scales. Use this when separate bar graphs are created for each cell cluster.

...

Additional arguments to pass to ggplot2, e.g. color, fill, size, linetype, etc.

Value

ggplot object

See also

calc_frequency(), plot_frequency()

Examples

# Plot clonotype abundance using all cells
plot_clonal_abundance(
  vdj_so,
  data_col = "clonotype_id"
)
#> Warning: Ignoring unknown parameters: `data_col`


# Plot clonotype abundance separately for each cell cluster
plot_clonal_abundance(
  vdj_sce,
  cluster_col = "orig.ident"
)


# Plot the frequency of each clonotype instead of percentage
plot_clonal_abundance(
  vdj_sce,
  cluster_col = "orig.ident",
  units = "frequency"
)


# Specify colors to use for each cell cluster
plot_clonal_abundance(
  vdj_so,
  cluster_col = "orig.ident",
  plot_colors = c(avid_1 = "blue", avid_2 = "red")
)


# Specify order to use for plotting cell clusters
plot_clonal_abundance(
  vdj_sce,
  cluster_col = "orig.ident",
  plot_lvls = c("avid_2", "avid_1")
)


# Specify the number of top clonotypes to plot
plot_clonal_abundance(
  vdj_so,
  n_clones = 5
)


#' # Create line graph
# use n_clones to set the number of clonotypes to label
plot_clonal_abundance(
  vdj_so,
  cluster_col = "orig.ident",
  method = "line",
  n_clones = 3
)