dittoPlot: Plots continuous data for customizeable cells'/samples'...

In dtm2451/dittoSeq: User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis

Description

Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis

Usage

dittoPlot(
  object,
  var,
  group.by,
  color.by = group.by,
  shape.by = NULL,
  split.by = NULL,
  extra.vars = NULL,
  cells.use = NULL,
  plots = c("jitter", "vlnplot"),
  multivar.aes = c("split", "group", "color"),
  multivar.split.dir = c("col", "row"),
  assay = .default_assay(object),
  slot = .default_slot(object),
  adjustment = NULL,
  swap.rownames = NULL,
  do.hover = FALSE,
  hover.data = var,
  color.panel = dittoColors(),
  colors = seq_along(color.panel),
  shape.panel = c(16, 15, 17, 23, 25, 8),
  theme = theme_classic(),
  main = "make",
  sub = NULL,
  ylab = "make",
  y.breaks = NULL,
  min = NA,
  max = NA,
  xlab = "make",
  x.labels = NULL,
  x.labels.rotate = NA,
  x.reorder = NULL,
  split.nrow = NULL,
  split.ncol = NULL,
  split.adjust = list(),
  do.raster = FALSE,
  raster.dpi = 300,
  jitter.size = 1,
  jitter.width = 0.2,
  jitter.color = "black",
  jitter.shape.legend.size = NA,
  jitter.shape.legend.show = TRUE,
  jitter.position.dodge = boxplot.position.dodge,
  boxplot.width = 0.2,
  boxplot.color = "black",
  boxplot.show.outliers = NA,
  boxplot.outlier.size = 1.5,
  boxplot.fill = TRUE,
  boxplot.position.dodge = vlnplot.width,
  boxplot.lineweight = 1,
  vlnplot.lineweight = 1,
  vlnplot.width = 1,
  vlnplot.scaling = "area",
  vlnplot.quantiles = NULL,
  ridgeplot.lineweight = 1,
  ridgeplot.scale = 1.25,
  ridgeplot.ymax.expansion = NA,
  ridgeplot.shape = c("smooth", "hist"),
  ridgeplot.bins = 30,
  ridgeplot.binwidth = NULL,
  add.line = NULL,
  line.linetype = "dashed",
  line.color = "black",
  legend.show = TRUE,
  legend.title = "make",
  data.out = FALSE
)

dittoRidgePlot(..., plots = c("ridgeplot"))

dittoRidgeJitter(..., plots = c("ridgeplot", "jitter"))

dittoBoxPlot(..., plots = c("boxplot", "jitter"))

Arguments

object	A Seurat, SingleCellExperiment, or SummarizedExperiment object.
var	Single string representing the name of a metadata or gene, OR a vector with length equal to the total number of cells/samples in the dataset. Alternatively, a string vector naming multiple genes or metadata. This is the primary data that will be displayed.
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 fills. Great for highlighting supersets or subgroups when wanted, but it defaults to group.by so this input can be skipped otherwise.
shape.by	Single string representing the name of a metadata to use for setting the shapes of the jitter points. When not provided, all cells/samples will be represented with dots.
split.by	1 or 2 strings naming discrete metadata to use for splitting the cells/samples into multiple plots with ggplot faceting. When 2 metadatas are named, c(row,col), the first is used as rows and the second is used for columns of the resulting grid. When 1 metadata is named, shape control can be achieved with split.nrow and split.ncol
extra.vars	String vector providing names of any extra metadata to be stashed in the dataframe supplied to ggplot(data). Useful for making custom spliting/faceting or other additional alterations after dittoSeq plot generation.
cells.use	String vector of cells'(/samples' for bulk data) names OR an integer vector specifying the indices of cells/samples which should be included. Alternatively, a Logical vector, the same length as the number of cells in the object, which sets which cells to include.
plots	String vector which sets the types of plots to include: possibilities = "jitter", "boxplot", "vlnplot", "ridgeplot". Order matters: c("vlnplot", "boxplot", "jitter") will put a violin plot in the back, boxplot in the middle, and then individual dots in the front. See details section for more info.
multivar.aes	"split", "group", or "color", the plot feature to utilize for displaying 'var' value when var is given multiple genes or metadata. When set to "split", inputs split.nrow, split.ncol, and split.adjust can be used to
multivar.split.dir	"row" or "col", sets the direction of faceting used for 'var' values when var is given multiple genes or metadata, when multivar.aes = "split", and when split.by is used to provide additional data to facet by.
assay, slot	single strings or integers (SCEs and SEs) or an optionally named vector of such values that set which expression data to use. See GeneTargeting for specifics and examples – Seurat and SingleCellExperiment objects deal with these differently, and functionality additions in dittoSeq have led to some minimal divergence from the native methodologies.
adjustment	When plotting gene expression / feature counts, should that data be used directly (default) or should it be adjusted to be "z-score": scaled with the scale() function to produce a relative-to-mean z-score representation "relative.to.max": divided by the maximum expression value to give percent of max values between [0,1]
swap.rownames	optionally named string or string vector. For SummarizedExperiment or SingleCellExperiment objects, its value(s) specifies the column name of rowData(object) to be used to identify features instead of rownames(object). When targeting multiple modalities (alternative experiments), names can be used to specify which level / alternative experiment (use 'main' for the top-level) individual values should be used for. See GeneTargeting for more specifics and examples.
do.hover	Logical. Default = FALSE. If set to TRUE: object will be converted to a ggplotly object so that data about individual cells will be displayed when you hover your cursor over the jitter points (assuming that there is a "jitter" in plots),
hover.data	String vector, a list of variable names, c("meta1","gene1","meta2",...) which determines what data to show upon hover when do.hover is set to TRUE.
color.panel	String vector which sets the colors to draw from for plot fills. Default = dittoColors().
colors	Integer vector, the indexes / order, of colors from color.panel to actually use. (Provides an alternative to directly modifying color.panel.)
shape.panel	Vector of integers corresponding to ggplot shapes which sets what shapes to use. When discrete groupings are supplied by shape.by, this sets the panel of shapes which will be used. When nothing is supplied to shape.by, only the first value is used. Default is a set of 6, c(16,15,17,23,25,8), the first being a simple, solid, circle.
theme	A ggplot theme which will be applied before dittoSeq adjustments. Default = theme_classic(). See https://ggplot2.tidyverse.org/reference/ggtheme.html for other options and ideas.
main	String, sets the plot title. Default = "make" and if left as make, a title will be automatically generated. To remove, set to NULL.
sub	String, sets the plot subtitle
ylab	String, sets the continuous-axis label (=y-axis for box and violin plots, x-axis for ridgeplots). Defaults to "var" or "var expression" if var is a gene.
y.breaks	Numeric vector, a set of breaks that should be used as major gridlines. c(break1,break2,break3,etc.).
min, max	Scalars which control the zoom of the plot. These inputs set the minimum / maximum values of the data to display. Default = NA, which allows ggplot to set these limits based on the range of all data being shown.
xlab	String which sets the grouping-axis label (=x-axis for box and violin plots, y-axis for ridgeplots). Set to NULL to remove.
x.labels	String vector, c("label1","label2","label3",...) which overrides the names of groupings.
x.labels.rotate	Logical which sets whether the labels should be rotated. Default: TRUE for violin and box plots, but FALSE for ridgeplots.
x.reorder	Integer vector. A sequence of numbers, from 1 to the number of groupings, for rearranging the order of x-axis groupings. Method: Make a first plot without this input. Then, treating the leftmost grouping as index 1, and the rightmost as index n. Values of x.reorder should be these indices, but in the order that you would like them rearranged to be. Recommendation for advanced users: If you find yourself coming back to this input too many times, an alternative solution that can be easier long-term is to make the target data into a factor, and to put its levels in the desired order: factor(data, levels = c("level1", "level2", ...)). metaLevels can be used to quickly get the identities that need to be part of this 'levels' input.
split.nrow, split.ncol	Integers which set the dimensions of faceting/splitting when a single metadata is given to split.by, or when multiple genes/metadata are given to var and multivar.aes = "split".
split.adjust	A named list which allows extra parameters to be pushed through to the faceting function call. List elements should be valid inputs to the faceting functions, e.g. 'list(scales = "free")'. For options, when giving 1 metadata to split.by or if faceting is by a set of vars, see facet_wrap, OR when giving 2 metadatas to split.by, see facet_grid.
do.raster	Logical. When set to TRUE, rasterizes the jitter plot layer, changing it from individually encoded points to a flattened set of pixels. This can be useful for editing in external programs (e.g. Illustrator) when there are many thousands of data points.
raster.dpi	Number indicating dots/pixels per inch (dpi) to use for rasterization. Default = 300.
jitter.size	Scalar which sets the size of the jitter shapes.
jitter.width	Scalar that sets the width/spread of the jitter in the x direction. Ignored in ridgeplots. Note for when color.by is used to split x-axis groupings into additional bins: ggplot does not shrink jitter widths accordingly, so be sure to do so yourself! Ideally, needs to be 0.5/num_subgroups.
jitter.color	String which sets the color of the jitter shapes
jitter.shape.legend.size	Scalar which changes the size of the shape key in the legend. If set to NA, jitter.size is used.
jitter.shape.legend.show	Logical which sets whether the shapes legend will be shown when its shape is determined by shape.by.
jitter.position.dodge	Scalar which adjusts the relative distance between jitter widths when multiple subgroups exist per group.by grouping (a.k.a. when group.by and color.by are not equal). Similar to boxplot.position.dodge input & defaults to the value of that input so that BOTH will actually be adjusted when only, say, boxplot.position.dodge = 0.3 is given.
boxplot.width	Scalar which sets the width/spread of the boxplot in the x direction
boxplot.color	String which sets the color of the lines of the boxplot
boxplot.show.outliers	Logical, whether outliers should by including in the boxplot. Default is FALSE when there is a jitter plotted, TRUE if there is no jitter.
boxplot.outlier.size	Scalar which adjusts the size of points used to mark outliers
boxplot.fill	Logical, whether the boxplot should be filled in or not. Known bug: when boxplot fill is turned off, outliers do not render.
boxplot.position.dodge	Scalar which adjusts the relative distance between boxplots when multiple are drawn per grouping (a.k.a. when group.by and color.by are not equal). By default, this input actually controls the value of jitter.position.dodge unless the jitter version is provided separately.
boxplot.lineweight	Scalar which adjusts the thickness of boxplot lines.
vlnplot.lineweight	Scalar which sets the thickness of the line that outlines the violin plots.
vlnplot.width	Scalar which sets the width/spread of violin plots in the x direction
vlnplot.scaling	String which sets how the widths of the of violin plots are set in relation to each other. Options are "area", "count", and "width". If the default is not right for your data, I recommend trying "width". For an explanation of each, see geom_violin.
vlnplot.quantiles	Single number or numeric vector of values in [0,1] naming quantiles at which to draw a horizontal line within each violin plot. Example: c(0.1, 0.5, 0.9)
ridgeplot.lineweight	Scalar which sets the thickness of the ridgeplot outline.
ridgeplot.scale	Scalar which sets the distance/overlap between ridgeplots. A value of 1 means the tallest density curve just touches the baseline of the next higher one. Higher numbers lead to greater overlap. Default = 1.25
ridgeplot.ymax.expansion	Scalar which adjusts the minimal space between the top-most grouping and the top of the plot in order to ensure that the curve is not cut off by the plotting grid. The larger the value, the greater the space requested. When left as NA, dittoSeq will attempt to determine an ideal value itself based on the number of groups & linear interpolation between these goal posts: 0.6 when g<=3, 0.1 when g==12, and 0.05 when g>=34, where g is the number of groups.
ridgeplot.shape	Either "smooth" or "hist", sets whether ridges will be smoothed (the typical, and default) versus rectangular like a histogram. (Note: as of the time shape "hist" was added, combination of jittered points is not supported by the stat_binline that dittoSeq relies on.)
ridgeplot.bins	Integer which sets how many chunks to break the x-axis into when ridgeplot.shape = "hist". Overridden by ridgeplot.binwidth when that input is provided.
ridgeplot.binwidth	Integer which sets the width of chunks to break the x-axis into when ridgeplot.shape = "hist". Takes precedence over ridgeplot.bins when provided.
add.line	numeric value(s) where one or multiple line(s) should be added
line.linetype	String which sets the type of line for add.line. Defaults to "dashed", but any ggplot linetype will work.
line.color	String that sets the color(s) of the add.line line(s)
legend.show	Logical. Whether the legend should be displayed. Default = TRUE.
legend.title	String or NULL, sets the title for the main legend which includes colors and data representations.
data.out	Logical. When set to TRUE, changes the output, from the plot alone, to a list containing the plot (p) and data (data).
...	arguments passed to dittoPlot by dittoRidgePlot, dittoRidgeJitter, and dittoBoxPlot wrappers. Options are all the ones above.

Details

The function creates a dataframe containing the metadata or expression data associated with the given var (or if a vector of data is provided, that data). On the discrete axis, data will be grouped by the metadata given to group.by and colored by the metadata given to color.by. The assay and slot inputs can be used to change what expression data is used when displaying gene expression. If a set of cells to use is indicated with the cells.use input, the data is subset to include only those cells before plotting.

The plots argument determines the types of data representation that will be generated, as well as their order from back to front. Options are "jitter", "boxplot", "vlnplot", and "ridgeplot". Inclusion of "ridgeplot" overrides "boxplot" and "vlnplot" presence and changes the plot to be horizontal.

When split.by is provided the name of a metadata containing discrete data, separate plots will be produced representing each of the distinct groupings of the split.by data.

dittoRidgePlot, dittoRidgeJitter, and dittoBoxPlot are included as wrappers of the basic dittoPlot function that simply change the default for the plots input to be "ridgeplot", c("ridgeplot","jitter"), or c("boxplot","jitter"), to make such plots even easier to produce.

Value

a ggplot where continuous data, grouped by sample, age, cluster, etc., shown on either the y-axis by a violin plot, boxplot, and/or jittered points, or on the x-axis by a ridgeplot with or without jittered points.

Alternatively when data.out=TRUE, a list containing the plot ("p") and the underlying data as a dataframe ("data").

Alternatively when do.hover = TRUE, a plotly converted version of the ggplot where additional data will be displayed when the cursor is hovered over jitter points.

Functions

• dittoRidgePlot(): Plots continuous data for customizeable cells'/samples' groupings horizontally in a density representation

• dittoRidgeJitter(): dittoRidgePlot, but with jitter overlaid

• dittoBoxPlot(): Plots continuous data for customizeable cells'/samples' groupings in boxplot form

Many characteristics of the plot can be adjusted using discrete inputs

The plots argument determines the types of data representation that will be generated, as well as their order from back to front. Options are "jitter", "boxplot", "vlnplot", and "ridgeplot".

Each plot type has specific associated options which are controlled by variables that start with their associated string. For example, all jitter adjustments start with "jitter.", such as jitter.size and jitter.width.

Inclusion of "ridgeplot" overrides "boxplot" and "vlnplot" presence and changes the plot to be horizontal.

Additionally:

• Colors can be adjusted with color.panel.

• Subgroupings: color.by can be utilized to split major group.by groupings into subgroups. When this is done in y-axis plotting, dittoSeq automatically ensures the centers of all geoms will align, but users will need to manually adjust jitter.width to less than 0.5/num_subgroups to avoid overlaps. There are also three inputs through which one can use to control geom-center placement, but the easiest way to do all at once so is to just adjust vlnplot.width! The other two: boxplot.position.dodge, and jitter.position.dodge.

• Line(s) can be added at single or multiple value(s) by providing these values to add.line. Linetype and color are set with line.linetype, which is "dashed" by default, and line.color, which is "black" by default.

• Titles and axes labels can be adjusted with main, sub, xlab, ylab, and legend.title arguments.

• The legend can be hidden by setting legend.show = FALSE.

• y-axis zoom and tick marks can be adjusted using min, max, and y.breaks.

• x-axis labels and groupings can be changed / reordered using x.labels and x.reorder, and rotation of these labels can be turned on/off with x.labels.rotate = TRUE/FALSE.

• Shapes used in conjunction with shape.by can be adjusted with shape.panel.

• Single or multiple additional per-cell features can be retrieved and stashed within the underlying data using extra.vars. This can be very useful for making manual additional alterations after dittoSeq plot generation.

Author(s)

Daniel Bunis

See Also

multi_dittoPlot for easy creation of multiple dittoPlots each focusing on a different var.

dittoPlotVarsAcrossGroups to create dittoPlots that show summarized expression (or values for metadata), accross groups, of multiple vars in a single plot.

dittoRidgePlot, dittoRidgeJitter, and dittoBoxPlot for shortcuts to a few 'plots' input shortcuts

Examples

example(importDittoBulk, echo = FALSE)
myRNA

# Basic dittoplot, with jitter behind a vlnplot (looks better with more cells)
dittoPlot(object = myRNA, var = "gene1", group.by = "timepoint")

# Color distinctly from the grouping variable using 'color.by'
dittoPlot(object = myRNA, var = "gene1", group.by = "timepoint",
    color.by = "conditions")
dittoPlot(object = myRNA, var = "gene1", group.by = "conditions",
    color.by = "timepoint")

# Update the 'plots' input to change / reorder the data representations
dittoPlot(myRNA, "gene1", "timepoint",
    plots = c("vlnplot", "boxplot", "jitter"))
dittoPlot(myRNA, "gene1", "timepoint",
    plots = c("ridgeplot", "jitter"))

### Provided wrappers enable certain easy adjustments of the 'plots' parameter.
# Quickly make a Boxplot
dittoBoxPlot(myRNA, "gene1", group.by = "timepoint")
# Quickly make a Ridgeplot, with or without jitter
dittoRidgePlot(myRNA, "gene1", group.by = "timepoint")
dittoRidgeJitter(myRNA, "gene1", group.by = "timepoint")

### Additional Functionality
# Modify the look with intuitive inputs
dittoPlot(myRNA, "gene1", "timepoint",
    plots = c("vlnplot", "boxplot", "jitter"),
    boxplot.color = "white",
    main = "CD3E",
    legend.show = FALSE)

# Data can also be split in other ways with 'shape.by' or 'split.by'
dittoPlot(object = myRNA, var = "gene1", group.by = "timepoint",
    plots = c("vlnplot", "boxplot", "jitter"),
    shape.by = "clustering",
    split.by = "SNP") # single split.by element
dittoPlot(object = myRNA, var = "gene1", group.by = "timepoint",
    plots = c("vlnplot", "boxplot", "jitter"),
    split.by = c("groups","SNP")) # row and col split.by elements

# Multiple genes or continuous metadata can also be plotted by giving them as
#   a vector to 'var'. One aesthetic of the plot will then be used to display
#   'var'-info, and you can control which (faceting / "split", x-axis grouping
#   / "group", or color / "color") with 'multivar.aes':
dittoPlot(object = myRNA, group.by = "timepoint",
    var = c("gene1", "gene2"))
dittoPlot(object = myRNA, group.by = "timepoint",
    var = c("gene1", "gene2"),
    multivar.aes = "group")
dittoPlot(object = myRNA, group.by = "timepoint",
    var = c("gene1", "gene2"),
    multivar.aes = "color")

# For faceting, instead of using 'split.by', the target data can alternatively
#   be given to 'extra.var' to have it added in the underlying dataframe, then
#   faceting can be added manually for extra flexibility
dittoPlot(myRNA, "gene1", "clustering",
    plots = c("vlnplot", "boxplot", "jitter"),
    extra.var = "SNP") + facet_wrap("SNP", ncol = 1, strip.position = "left")

dtm2451/dittoSeq documentation built on May 5, 2024, 11:19 a.m.