multi_dittoPlot {dittoSeq}R Documentation

Generates multiple dittoPlots arranged into a grid.

Description

Generates multiple dittoPlots arranged into a grid.

Usage

multi_dittoPlot(
  object,
  vars,
  group.by,
  color.by = group.by,
  legend.show = FALSE,
  ncol = 3,
  nrow = NULL,
  main = "var",
  ylab = NULL,
  xlab = NULL,
  OUT.List = FALSE,
  ...
)

Arguments

object

the Seurat or SingleCellExperiment object to draw from

vars

c("var1","var2","var3",...). A vector of gene or metadata names from which to generate the separate plots

group.by

String representing the name of a metadata to use for separating the cells/samples into discrete groups.

color.by

String representing the name of a metadata to use for setting color. Default = group.by.

ncol, nrow

Integers which set how many plots will be arranged per column or per row. Default = 3 columns aand however many rows are required.

Set both to NULL to have the grid.arrange function figure out what might be most "square" on its own.

main, ylab

String which sets whether / how plot titles or y-axis labels should be added to each individual plot

  • When set to "var", the vars names alone will be used.

  • When set to "make", the default dittoPlot behavior will be observed: Equivalent to "make" for main, but for y-axis labels, gene vars will become "'var' expression".

  • When set as any other string, that string will be used as the title / y-axis label for every plot.

  • When set to NULL, titles / axes labels will not be added.

xlab, legend.show, ...

other paramters passed along to dittoPlot.

OUT.List

Logical. (Default = FALSE) When set to TRUE, a list of the individual plots, named by the vars being shown in each, is output instead of the combined multi-plot.

Value

Given multiple 'var' parameters, this function will output a dittoPlot for each one, arranged into a grid, just with some slight tweaks to the defaults. If OUT.list was set to TRUE, the list of individual plots is output instead of the combined multi-plot. All parameters that can be adjusted in dittoPlot can be adjusted here.

Author(s)

Daniel Bunis

See Also

dittoPlot for the single plot version of this function

Examples

# dittoSeq handles bulk and single-cell data quit similarly.
# The SingleCellExperiment object structure is used for both,
# but all functions can be used similarly directly on Seurat
# objects as well.

example(importDittoBulk, echo = FALSE)
myRNA

genes <- getGenes(myRNA)[1:4]
multi_dittoPlot(myRNA, genes, group.by = "clustering")

# violin-plots in front is often better for large single-cell datasets,
# but we cn change the order with 'plots'
multi_dittoPlot(myRNA, genes, "clustering",
    plots = c("vlnplot","boxplot","jitter"))

#To make it output a grid that is 2x2, to add y-axis labels
# instead of titles, and to show legends...
multi_dittoPlot(myRNA, genes, "clustering",
    nrow = 2, ncol = 2,           #Make grid 2x2 (only one of these needed)
    main = NULL, ylab = "make",   #Add y axis labels instead of titles
    legend.show = TRUE)           #Show legends

# We can also facet with 'split.by'
multi_dittoPlot(myRNA, genes, "clustering",
    split.by = "SNP")
[Package dittoSeq version 1.0.2 Index]