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ClonalResidencyPlot

Source: R/clonalcompositionplot.R
ClonalResidencyPlot.Rd

Plot the residency of the clones in different samples.

Usage

ClonalResidencyPlot(
  data,
  clone_call = "aa",
  chain = "both",
  plot_type = c("scatter", "venn", "upset"),
  group_by = "Sample",
  groups = NULL,
  facet_by = NULL,
  split_by = NULL,
  split_by_sep = "_",
  scatter_cor = "pearson",
  scatter_size_by = c("max", "total"),
  order = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  ...
)

Arguments

data

The product of scRepertoire::combineTCR, scRepertoire::combineTCR, or scRepertoire::combineExpression.

clone_call

How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data

chain

indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL"

plot_type

The type of plot to use. Default is "scatter". Possible values are "scatter", "venn", and "upset".

group_by

The column name in the meta data to group the cells. Default: "Sample"

groups

The groups to compare. Default is NULL. If NULL, all the groups in group_by will be compared. Note that for "scatter" plot, only two groups can be compared. So when there are more than two groups, the combination of the pairs will be used. For "scatter" plot, the groups can be specified as the comparisons separated by ":", e.g. "L:B", "Y:X".

facet_by

The column name in the meta data to facet the plots. Default: NULL

split_by

The column name in the meta data to split the plots. Default: NULL

split_by_sep

The separator used to concatenate the split_by when multiple columns are used.

scatter_cor

The correlation method to use for the scatter plot. Default is "pearson".

scatter_size_by

The size of the points in the scatter plot. Default is "max". Possible values are "max" and "total".

  • "max" - The max size of the clone in the two groups.

  • "total" - The total size of the clone in the two groups.

order

The order of the x-axis items or groups. Default is an empty list. It should be a list of values. The names are the column names, and the values are the order.

combine

Whether to combine the plots into a single plot. Default is TRUE.

nrow

The number of rows in the combined plot. Default is NULL.

ncol

The number of columns in the combined plot. Default is NULL.

byrow

Whether to fill the combined plot by row. Default is TRUE.

...

Other arguments passed to the specific plot function.

Value

A ggplot object or a list if combine is FALSE

Examples

# \donttest{
set.seed(8525)
data(contig_list, package = "scRepertoire")
data <- scRepertoire::combineTCR(contig_list,
    samples = c("P17B", "P17L", "P18B", "P18L", "P19B","P19L", "P20B", "P20L"))
data <- scRepertoire::addVariable(data,
    variable.name = "Type",
    variables = rep(c("B", "L", "X", "Y"), 2)
)
data <- scRepertoire::addVariable(data,
    variable.name = "Subject",
    variables = rep(c("P17", "P18", "P19", "P20"), each = 2)
)

ClonalResidencyPlot(data, groups = c("P18B", "P18L"))
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).

ClonalResidencyPlot(data, group_by = "Type", groups = c("L", "B"),
 split_by = "Subject")
#> Warning: [ClonalResidencyPlot] Not both groups 'L, B' is not present in the data for 'P18'. Skipping.
#> Warning: [ClonalResidencyPlot] Not both groups 'L, B' is not present in the data for 'P20'. Skipping.
#> Warning: Removed 40 rows containing missing values or values outside the scale range
#> (`geom_point()`).

ClonalResidencyPlot(data, group_by = "Type", groups = c("L:B", "Y:X"),
 split_by = "Subject")
#> Warning: [ClonalResidencyPlot] Not both groups 'Y, X' is not present in the data for 'P17'. Skipping.
#> Warning: [ClonalResidencyPlot] Not both groups 'L, B' is not present in the data for 'P18'. Skipping.
#> Warning: [ClonalResidencyPlot] Not both groups 'Y, X' is not present in the data for 'P19'. Skipping.
#> Warning: [ClonalResidencyPlot] Not both groups 'L, B' is not present in the data for 'P20'. Skipping.
#> Warning: Removed 40 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).

ClonalResidencyPlot(data, plot_type = "venn", groups = c("B", "L"),
 group_by = "Type", split_by = "Subject")

ClonalResidencyPlot(data, plot_type = "upset", groups = c("P18B", "P18L"))

# }