plot_numerical: Plot numerical single-cell data

In rnabioco/AVIDtools: A collection of single-cell V(D)J tools

Plot numerical single-cell data

Description

Visualize numerical single-cell data by creating a histogram, density plot, violin plots, or boxplots. When plotting V(D)J data, values can be plotted separately for each chain or summarized and plotted for each cell.

Usage

plot_histogram(
  input,
  data_col,
  cluster_col = NULL,
  group_col = NULL,
  method = "histogram",
  top = NULL,
  other_label = "other",
  units = "frequency",
  plot_colors = NULL,
  plot_lvls = NULL,
  trans = "identity",
  panel_nrow = NULL,
  panel_scales = "fixed",
  na_color = "grey80",
  n_label = NULL,
  label_params = list(),
  ...,
  per_chain = FALSE,
  chain = NULL,
  chain_col = global$chain_col,
  summary_fn = mean,
  sep = global$sep
)

plot_violin(
  input,
  data_col,
  cluster_col = NULL,
  group_col = NULL,
  method = "violin",
  top = NULL,
  other_label = "other",
  plot_colors = NULL,
  plot_lvls = NULL,
  trans = "identity",
  panel_nrow = NULL,
  panel_scales = "free_x",
  na_color = "grey80",
  n_label = NULL,
  label_params = list(),
  ...,
  per_chain = FALSE,
  chain = NULL,
  chain_col = global$chain_col,
  summary_fn = mean,
  sep = global$sep
)

Arguments

input	Single cell object or data.frame, if a data.frame is provided, cell barcodes should be stored as row names.
data_col	meta.data column containing data to plot
cluster_col	meta.data column containing cluster IDs to use for grouping cells for plotting
group_col	meta.data column to use for grouping clusters into separate panels
method	Method to use for plotting, possible values include, 'histogram', 'density', 'boxplot', or 'violin'
top	To only show the top cell groups, provide one of the following, all other cells will be labeled using the value provided to the other_label argument. If NULL this will be automatically set. Integer specifying the number of top groups to show Vector specifying the names of cell groups to show
other_label	Label to use for 'other' cells when top is specified, if NULL all cell groups will be shown.
units	Units to use for y-axis when method is 'histogram'. Use 'frequency' to show the number of values or 'percent' to show the percentage of total values.
plot_colors	Character vector specifying colors to use for cell clusters specified by cluster_col. When cluster_col is NULL, plot colors can be directly modified with the ggplot2 parameters color and fill, e.g. fill = "red", color = "black"
plot_lvls	Character vector containing order to use for plotting cell clusters specified by cluster_col
trans	Transformation to use when plotting data, e.g. 'log10'. By default values are not transformed, refer to ggplot2::continuous_scale() for more options.
panel_nrow	The number of rows to use for arranging plot panels
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.
na_color	Color to use for missing values. If plotting V(D)J data, cells lacking data will be plotted as NAs.
n_label	Location on plot where n label should be added, this can be any combination of the following: 'corner', display the total number of cells plotted in the top right corner, the position of the label can be modified by passing x and y specifications with the label_params argument 'axis', display the number of cells plotted for each group shown on the x-axis 'legend', display the number of cells plotted for each group shown in the plot legend 'none', do not display the number of cells plotted
label_params	Named list providing additional parameters to modify n label aesthetics, e.g. list(size = 4, color = "red")
...	Additional arguments to pass to ggplot2, e.g. color, fill, size, linetype, etc.
per_chain	If TRUE values will be plotted for each chain, i.e. each data point represents a chain. If FALSE values will be summarized for each cell using summary_fn before plotting, i.e. each data point represents a cell.
chain	Chain(s) to use for filtering data before plotting. If NULL data will not be filtered based on chain.
chain_col	meta.data column containing chains for each cell
summary_fn	Function to use for summarizing values when per_chain is FALSE, can be either a function, e.g. mean, or a purrr-style lambda, e.g. ~ mean(.x, na.rm = TRUE) where .x refers to the column. If NULL, the mean will be calculated.
sep	Separator used for storing per-chain V(D)J data for each cell

Value

ggplot object

See Also

summarize_vdj() for more examples on how per-chain data can be summarized for each cell

Examples

# Create histogram
plot_histogram(
  vdj_sce,
  data_col    = "reads",
  cluster_col = "orig.ident",
  trans       = "log10"
)

# Create violin plots
plot_violin(
  vdj_sce,
  data_col    = "nFeature_RNA",
  cluster_col = "orig.ident"
)

rnabioco/AVIDtools documentation built on Oct. 28, 2023, 10:23 a.m.