Plot numerical single-cell data

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

Examples

# Create histogram
plot_histogram(
  vdj_sce,
  data_col    = "reads",
  cluster_col = "orig.ident",
  trans       = "log10"
)
#> Warning: Removed 133 rows containing missing values
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


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

Usage

Arguments

Value

See also

Examples