dittoScatterPlot {dittoSeq} | R Documentation

## Show RNAseq data overlayed on a scatter plot

### Description

Show RNAseq data overlayed on a scatter plot

### Usage

    dittoScatterPlot(
      object,
      x.var,
      y.var,
      color.var = NULL,
      shape.by = NULL,
      split.by = NULL,
      extra.vars = NULL,
      cells.use = NULL,
      show.others = FALSE,
      split.show.all.others = TRUE,
      size = 1,
      opacity = 1,
      color.panel = dittoColors(),
      colors = seq_along(color.panel),
      split.nrow = NULL,
      split.ncol = NULL,
      split.adjust = list(),
      assay.x = .default_assay(object),
      slot.x = .default_slot(object),
      adjustment.x = NULL,
      assay.y = .default_assay(object),
      slot.y = .default_slot(object),
      adjustment.y = NULL,
      assay.color = .default_assay(object),
      slot.color = .default_slot(object),
      adjustment.color = NULL,
      assay.extra = .default_assay(object),
      slot.extra = .default_slot(object),
      adjustment.extra = NULL,
      swap.rownames = NULL,
      shape.panel = c(16, 15, 17, 23, 25, 8),
      rename.color.groups = NULL,
      rename.shape.groups = NULL,
      min.color = "#F0E442",
      max.color = "#0072B2",
      min = NULL,
      max = NULL,
      order = c("unordered", "increasing", "decreasing"),
      xlab = x.var,
      ylab = y.var,
      main = "make",
      sub = NULL,
      theme = theme_bw(),
      do.hover = FALSE,
      hover.data = NULL,
      hover.assay = .default_assay(object),
      hover.slot = .default_slot(object),
      hover.adjustment = NULL,
      do.contour = FALSE,
      contour.color = "black",
      contour.linetype = 1,
      add.trajectory.lineages = NULL,
      add.trajectory.curves = NULL,
      trajectory.cluster.meta,
      trajectory.arrow.size = 0.15,
      do.letter = FALSE,
      do.ellipse = FALSE,
      do.label = FALSE,
      labels.size = 5,
      labels.highlight = TRUE,
      labels.repel = TRUE,
      labels.split.by = split.by,
      legend.show = TRUE,
      legend.color.title = color.var,
      legend.color.size = 5,
      legend.color.breaks = waiver(),
      legend.color.breaks.labels = waiver(),
      legend.shape.title = shape.by,
      legend.shape.size = 5,
      do.raster = FALSE,
      raster.dpi = 300,
      data.out = FALSE
    )

### Arguments

`object` | A Seurat, SingleCellExperiment, or SummarizedExperiment object.
`x.var, y.var` | Single string giving a gene or metadata that will be used for the x- and y-axis of the scatterplot. Note: must be continuous. Alternatively, can be a directly supplied numeric vector of length equal to the total number of cells/samples in `object`.
`color.var` | Single string giving a gene or metadata that will set the color of cells/samples in the plot. Alternatively, can be a directly supplied numeric or string vector or a factor of length equal to the total number of cells/samples in `object`.
`shape.by` | Single string giving a metadata (Note: must be discrete.) that will set the shape of cells/samples in the plot. Alternatively, can be a directly supplied string vector or a factor of length equal to the total number of cells/samples in `object`.
`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 alterations after dittoSeq plot generation.
`cells.use` | String vector of cells'/samples' 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.
`show.others` | Logical. FALSE by default, whether other cells should be shown in the background in light gray.
`split.show.all.others` | Logical which sets whether gray "others" cells of facets should include all cells of other facets (`TRUE`) versus just cells left out by `cell.use` (`FALSE`).
`size` | Number which sets the size of data points. Default = 1.
`opacity` | Number between 0 and 1. Great for when you have MANY overlapping points, this sets how solid the points should be: 1 = not see-through at all. 0 = invisible. Default = 1. (In terms of typical ggplot variables, = alpha)
`color.panel` | String vector which sets the colors to draw from. `dittoColors()` by default, see `dittoColors` for contents.
`colors` | Integer vector, the indexes / order, of colors from color.panel to actually use
`split.nrow, split.ncol` | Integers which set the dimensions of faceting/splitting when a single metadata is given to `split.by`.
`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`, see `facet_wrap`, OR when giving 2 metadatas to `split.by`, see `facet_grid`.
`assay.x, assay.y, assay.color, assay.extra, slot.x, slot.y, slot.color, slot.extra, adjustment.x, adjustment.y, adjustment.color, adjustment.extra` | assay, slot, and adjustment set which data to use when the axes, coloring, or `extra.vars` are based on expression/counts data. See `gene` for additional information.
`swap.rownames` | String. For SummarizeedExperiment or SingleCellExperiment objects, the column name of rowData(object) to be used to identify features instead of rownames(object).
`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. 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. Note: Unfortunately, shapes can be hard to see when points are on top of each other & they are more slowly processed by the brain. For these reasons, even as a color blind person myself writing this code, I recommend use of colors for variables with many discrete values.
`rename.color.groups, rename.shape.groups` | String vector containing new names for the identities of the color or shape overlay groups.
`min.color` | color for `min` value of `color.var` data. Default = yellow
`max.color` | color for `max` value of `color.var` data. Default = blue
`min, max` | Number which sets the values associated with the minimum or maximum colors.
`order` | String. If the data should be plotted based on the order of the color data, sets whether to plot in "increasing" or "decreasing" order.
`xlab, ylab` | Strings which set the labels for the axes. To remove, set to `NULL`.
`main` | String, sets the plot title. A default title is automatically generated if based on `color.var` and `shape.by` when either are provided. To remove, set to `NULL`.
`sub` | String, sets the plot subtitle.
`theme` | A ggplot theme which will be applied before dittoSeq adjustments. Default = `theme_bw()`. See https://ggplot2.tidyverse.org/reference/ggtheme.html for other options and ideas.
`do.hover` | Logical which controls whether the object will be converted to a plotly object so that data about individual points will be displayed when you hover your cursor over them. `hover.data` argument is used to determine what data to use.
`hover.data` | String vector of gene and metadata names, example: `c("meta1","gene1","meta2","gene2")` which determines what data to show on hover when `do.hover` is set to `TRUE`.
`hover.assay, hover.slot, hover.adjustment` | Similar to the x, y, color, and extra versions, when showing expression data upon hover, these set what data will be shown.
`do.contour` | Logical. Whether density-based contours should be displayed.
`contour.color` | String that sets the color(s) of the `do.contour` contours.
`contour.linetype` | String or numeric which sets the type of line used for `do.contour` contours. Defaults to "solid", but see `linetype` for other options.
`add.trajectory.lineages` | List of vectors representing trajectory paths, each from start-cluster to end-cluster, where vector contents are the names of clusters provided in the `trajectory.cluster.meta` input. If the `slingshot` package was used for trajectory analysis, you can provide `add.trajectory.lineages = slingLineages('object')`.
`add.trajectory.curves` | List of matrices, each representing coordinates for a trajectory path, from start to end, where matrix columns represent x and y coordinates of the paths.
`trajectory.cluster.meta` | String name of metadata containing the clusters that were used for generating trajectories. Required when plotting trajectories using the `add.trajectory.lineages` method. Names of clusters inside the metadata should be the same as the contents of `add.trajectory.lineages` vectors.
`trajectory.arrow.size` | Number representing the size of trajectory arrows, in inches. Default = 0.15.
`do.letter` | Logical which sets whether letters should be added on top of the colored dots. For extended colorblindness compatibility. NOTE: `do.letter` is ignored if `do.hover = TRUE` or `shape.by` is provided a metadata because lettering is incompatible with plotly and with changing the dots' to be different shapes.
`do.ellipse` | Logical. Whether the groups should be surrounded by median-centered ellipses.
`do.label` | Logical. Whether to add text labels near the center (median) of clusters for grouping vars.
`labels.size` | Size of the the labels text
`labels.highlight` | Logical. Whether the labels should have a box behind them
`labels.repel` | Logical, that sets whether the labels' placements will be adjusted with ggrepel to avoid intersections between labels and plot bounds. TRUE by default.
`labels.split.by` | String of one or two metadata names which controls the facet-split calculations for label placements. Defaults to `split.by`, so generally there is no need to adjust this except when you are utilizing the `extra.vars` input to achieve manual faceting control.
`legend.show` | Logical. Whether any legend should be displayed. Default = `TRUE`.
`legend.color.title, legend.shape.title` | Strings which set the title for the color or shape legends.
`legend.color.size, legend.shape.size` | Numbers representing the size at which shapes should be plotted in the color and shape legends (for discrete variable plotting). Default = 5. *Enlarging the icons in the colors legend is incredibly helpful for making colors more distinguishable by color blind individuals.
`legend.color.breaks` | Numeric vector which sets the discrete values to label in the color-scale legend for continuous data.
`legend.color.breaks.labels` | String vector, with same length as `legend.breaks`, which sets the labels for the tick marks of the color-scale.
`do.raster` | Logical. When set to `TRUE`, rasterizes the internal 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.
`data.out` | Logical. When set to `TRUE`, changes the output, from the plot alone, to a list containing the plot ("p"), a data.frame containing the underlying data for target cells ("Target_data"), and a data.frame containing the underlying data for non-target cells ("Others_data").

### Details

This function creates a dataframe with X, Y, color, shape, and faceting data determined by `x.var`, `y.var`, `color.var`, `shape.var`, and `split.by`. Any extra gene or metadata requested with `extra.var` is added as well. For expression/counts data, `assay`, `slot`, and `adjustment` inputs (`.x`, `.y`, and `.color`) can be used to change which data is used, and if it should be adjusted in some way.

Next, if a set of cells or samples to use is indicated with the `cells.use` input, then the dataframe is split into `Target_data` and `Others_data` based on subsetting by the target cells/samples.

Finally, a scatter plot is created using these dataframes. Non-target cells are colored in gray if `show.others=TRUE`, and target cell data is displayed on top, colored and shaped based on the `color.var`- and `shape.by`-associated data. If `split.by` was used, the plot will be split into a matrix of panels based on the associated groupings.

### Value

a ggplot scatterplot where colored dots and/or shapes represent individual cells/samples. X and Y axes can be gene expression, numeric metadata, or manually supplied values.

Alternatively, if `data.out=TRUE`, a list containing three slots is output: the plot (named 'p'), a data.table containing the underlying data for target cells (named 'Target_data'), and a data.table containing the underlying data for non-target cells (named 'Others_data').

Alternatively, if `do.hover` is set to `TRUE`, the plot is coverted from ggplot to plotly & cell/sample information, determined by the `hover.data` input, is retrieved, added to the dataframe, and displayed upon hovering the cursor over the plot.

### Many characteristics of the plot can be adjusted using discrete inputs

- `size` and `opacity` can be used to adjust the size and transparency of the data points.

- Colors used can be adjusted with `color.panel` and/or `colors` for discrete data, or `min`, `max`, `min.color`, and `max.color` for continuous data.

- Shapes used can be adjusted with `shape.panel`.

- Color and shape labels can be changed using `rename.color.groups` and `rename.shape.groups`.

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

- Legends can also be adjusted in other ways, using variables that all start with "`legend.`" for easy tab completion lookup.

### Author(s)

Daniel Bunis and Jared Andrews

### See Also

`getGenes` and `getMetas` to see what the `x.var`, `y.var`, `color.var`, `shape.by`, and `hover.data` options are of an `object`.

`dittoDimPlot` for making very similar data representations, but where dimensionality reduction (PCA, t-SNE, UMAP, etc.) dimensions are the scatterplot axes.

`dittoDimHex` and `dittoScatterHex` for showing very similar data representations, but where nearby cells are summarized together in hexagonal bins.

### Examples

    example(importDittoBulk, echo = FALSE)
    myRNA

    # Mock up some nCount_RNA and nFeature_RNA metadata
    #  == the default way to extract
    myRNA$nCount_RNA <- runif(60,200,1000)
    myRNA$nFeature_RNA <- myRNA$nCount_RNA*runif(60,0.95,1.05)
    # and also percent.mito metadata
    myRNA$percent.mito <- sample(c(runif(50,0,0.05),runif(10,0.05,0.2)))

    dittoScatterPlot(
        myRNA, x.var = "nCount_RNA", y.var = "nFeature_RNA")

    # Shapes or colors can be overlaid representing discrete metadata
    #   or (only colors) continuous metadata / expression data by providing
    #   metadata or gene names to 'color.var' and 'shape.by'
    dittoScatterPlot(
        myRNA, x.var = "gene1", y.var = "gene2",
        color.var = "groups",
        shape.by = "SNP",
        size = 3)
    dittoScatterPlot(
        myRNA, x.var = "gene1", y.var = "gene2",
        color.var = "gene3")

    # Note: scatterplots like this can be very useful for dataset QC, especially
    #   with percentage of mitochondrial reads as the color overlay.
    dittoScatterPlot(myRNA,
        x.var = "nCount_RNA", y.var = "nFeature_RNA",
        color.var = "percent.mito")

    # Data can be "split" or faceted by a discrete variable as well.
    dittoScatterPlot(myRNA, x.var = "gene1", y.var = "gene2",
        split.by = "timepoint") # single split.by element
    dittoScatterPlot(myRNA, x.var = "gene1", y.var = "gene2",
        split.by = c("groups","SNP")) # row and col split.by elements
    # OR with 'extra.vars' plus manually faceting for added control
    dittoScatterPlot(myRNA, x.var = "gene1", y.var = "gene2",
        extra.vars = c("SNP")) +
        facet_wrap("SNP", ncol = 1, strip.position = "left")

    # Countours can also be added to help illumunate overlapping samples
    dittoScatterPlot(myRNA, x.var = "gene1", y.var = "gene2",
        do.contour = TRUE)

[Package dittoSeq version 1.4.4 Index]