Plot continuous V(D)J data

Usage

plot_vdj(
  input,
  data_col,
  per_cell = FALSE,
  summary_fn = mean,
  cluster_col = NULL,
  group_col = NULL,
  chain = NULL,
  method = "histogram",
  units = "frequency",
  plot_colors = NULL,
  plot_lvls = names(plot_colors),
  trans = "identity",
  panel_nrow = NULL,
  panel_scales = "free_x",
  chain_col = "chains",
  sep = ";",
  ...
)

Arguments

input

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

data_col

meta.data column(s) containing continuous V(D)J data to plot

per_cell

Should values be plotted per cell, i.e. each data point would represent one cell. If TRUE, values will be summarized for each cell using summary_fn. If FALSE, values will be plotted for each chain.

summary_fn

Function to use for summarizing values when per_cell is TRUE, possible values 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.

cluster_col

meta.data column containing cluster IDs to use for grouping cells for plotting

group_col

meta.dats column to use for grouping clusters present in cluster_col

chain

Chain(s) to use for filtering data before plotting. If NULL data will not be filtered based on chain.

method

Method to use for plotting, possible values are:

'histogram'
'density'
'boxplot'
'violin'

units

Units to use for y-axis when method is set to 'histogram'. Use 'frequency' to show 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 for 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.

chain_col

meta.data column containing chains for each cell

sep

Separator used for storing per-chain V(D)J data for each cell

...

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

Value

ggplot object

Examples

# Create histogram
plot_vdj(
  vdj_sce,
  data_col = "reads"
)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Create boxplots
plot_vdj(
  vdj_sce,
  data_col = "reads",
  method = "boxplot"
)


# Pass additional arguments to ggplot2
plot_vdj(
  vdj_so,
  data_col = "reads",
  color = "red",
  bins = 25
)


# Compare cell clusters
plot_vdj(
  vdj_sce,
  data_col = "cdr3_length",
  cluster_col = "orig.ident",
  method = "violin"
)


# log10 transform the axis
plot_vdj(
  vdj_so,
  data_col = "reads",
  cluster_col = "orig.ident",
  trans = "log10"
)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Express y-axis units as percent of total values
plot_vdj(
  vdj_sce,
  data_col = "umis",
  cluster_col = "orig.ident",
  units = "percent"
)
#> Warning: The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(count)` instead.
#> ℹ The deprecated feature was likely used in the djvdj package.
#>   Please report the issue at <https://github.com/rnabioco/djvdj/issues>.
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Only plot values for heavy chains
plot_vdj(
  vdj_so,
  data_col = "umis",
  chain = "IGH"
)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Plot the median number of reads for each cell
plot_vdj(
  vdj_sce,
  data_col = "reads",
  per_cell = TRUE,
  summary_fn = stats::median
)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Set colors for cell clusters
plot_vdj(
  vdj_so,
  data_col = "cdr3_length",
  cluster_col = "orig.ident",
  plot_colors = c(avid_1 = "red", avid_2 = "purple")
)
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.


# Set order to use for plotting cell clusters
plot_vdj(
  vdj_sce,
  data_col = "cdr3_length",
  cluster_col = "orig.ident",
  plot_lvls = c("avid_2", "avid_1"),
  method = "boxplot"
)

Plot continuous V(D)J data

Usage

Arguments

Value

See also

Examples