dittoBarPlot {dittoSeq} | R Documentation

## Outputs a stacked bar plot to show the percent composition of samples, groups, clusters, or other groupings

### Description

Outputs a stacked bar plot to show the percent composition of samples, groups, clusters, or other groupings

### Usage

    dittoBarPlot(
      object,
      var,
      group.by,
      scale = c("percent", "count"),
      split.by = NULL,
      cells.use = NULL,
      retain.factor.levels = FALSE,
      data.out = FALSE,
      do.hover = FALSE,
      color.panel = dittoColors(),
      colors = seq_along(color.panel),
      split.nrow = NULL,
      split.ncol = NULL,
      split.adjust = list(),
      y.breaks = NA,
      min = 0,
      max = NULL,
      var.labels.rename = NULL,
      var.labels.reorder = NULL,
      x.labels = NULL,
      x.labels.rotate = TRUE,
      x.reorder = NULL,
      theme = theme_classic(),
      xlab = group.by,
      ylab = "make",
      main = "make",
      sub = NULL,
      legend.show = TRUE,
      legend.title = NULL
    )

### Arguments

`object` | A Seurat, SingleCellExperiment, or SummarizedExperiment object.
`var` | String name of a metadata that contains discrete data, or a factor or vector containing such data for all cells/samples in the target `object`.
`group.by` | String name of a metadata to use for separating the cells/samples into discrete groups.
`scale` | "count" or "percent". Sets whether data should be shown as counts versus percentage.
`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`
`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. Note: When `cells.use` is combined with `scale = "percent"`, left out cells are not considered in calculating percentages. Percents will always total to 1.
`retain.factor.levels` | Logical which controls whether factor identities of `var` and `group.by` data should be respected. Set to TRUE to faithfully reflect ordering of groupings encoded in factor levels, but Note that this will also force retention of groupings that could otherwise be removed via `cells.use`.
`data.out` | Logical. When set to `TRUE`, changes the output, from the plot alone, to a list containing the plot ("p") and a data.frame ("data") containing the underlying data.
`do.hover` | Logical which sets whether the ggplot output should be converted to a ggplotly object with data about individual bars displayed when you hover your cursor over them.
`color.panel` | String vector which sets the colors to draw from. `dittoColors()` by default.
`colors` | Integer vector, which sets the indexes / order, of colors from color.panel to actually use. (Provides an alternative to directly modifying `color.panel`.)
`split.nrow` | Integers which set the dimensions of faceting/splitting when a single metadata is given to `split.by`.
`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`.
`y.breaks` | Numeric vector which sets the plot's tick marks / 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 y-axis. Default = set based on the limits of the data, 0 to 1 for `scale = "percent"`, or 0 to maximum count for 0 to 1 for `scale = "count"`.
`var.labels.rename` | String vector for renaming the distinct identities of `var` values. Hint: use `metaLevels` or `unique(<var-data>)` to assess current values.
`var.labels.reorder` | Integer vector. A sequence of numbers, from 1 to the number of distinct `var` value identities, for rearranging the order of labels' groupings within the plot. Method: Make a first plot without this input. Then, treating the top-most grouping as index 1, and the bottom-most as index n. Values of `var.labels.reorder` should be these indices, but in the order that you would like them rearranged to be.
`x.labels` | String vector which will replace the x-axis groupings' labels. Regardless of `x.reorder`, the first component of `x.labels` sets the name for the left-most x-axis grouping.
`x.labels.rotate` | Logical which sets whether the x-axis grouping labels should be rotated.
`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.
`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.
`xlab` | String which sets the x-axis title. Default is `group.by` so it defaults to the name of the grouping information. Set to `NULL` to remove.
`ylab` | String which sets the y-axis title. Default = "make" and if left as make, a title will be automatically generated.
`main` | String, sets the plot title
`sub` | String, sets the plot subtitle
`legend.show` | Logical which sets whether the legend should be displayed.
`legend.title` | String which adds a title to the legend.

### Details

The function creates a dataframe containing counts and percent makeup of `var` identities for each x-axis grouping (determined by the `group.by` input). If a set of cells/samples to use is indicated with the `cells.use` input, only those cells/samples are used for counts and percent makeup calculations. Then, a vertical bar plot is generated (`ggplot2::geom_col()`) showing either percent makeup if `scale = "percent"`, which is the default, or raw counts if `scale = "count"`.

### Value

A ggplot plot where discrete data, grouped by sample, condition, cluster, etc. on the x-axis, is shown on the y-axis as either counts or percent-of-total-per-grouping in a stacked barplot.

Alternatively, if `data.out = TRUE`, a list containing the plot ("p") and a dataframe of the underlying data ("data").

Alternatively, if `do.hover = TRUE`, a plotly conversion of the ggplot output in which underlying data can be retrieved upon hovering the cursor over the plot.

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

- Colors can be adjusted with `color.panel` and/or `colors`.

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

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

- The legend can be removed by setting `legend.show = FALSE`.

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

- y-axis `var`-group labels and their order can be changed / reordered using `var.labels` and `var.labels.reorder`.

### Author(s)

Daniel Bunis

### See Also

`dittoFreqPlot` for a data representation that focuses on pre-sample frequencies of each the `var`-data values individually, rather than emphasizing total makeup of samples/groups.

### Examples

    example(importDittoBulk, echo = FALSE)
    myRNA

    dittoBarPlot(myRNA, "clustering", group.by = "groups")
    dittoBarPlot(myRNA, "clustering", group.by = "groups",
        scale = "count")

    # Reordering the x-axis groupings to have "C" (#3) come first
    dittoBarPlot(myRNA, "clustering", group.by = "groups",
        x.reorder = c(3,1,2,4))

    ### Accessing underlying data:
    # as dataframe
    dittoBarPlot(myRNA, "clustering", group.by = "groups",
        data.out = TRUE)
    # through hovering the cursor over the relevant parts of the plot
    if (requireNamespace("plotly", quietly = TRUE)) {
        dittoBarPlot(myRNA, "clustering", group.by = "groups",
            do.hover = TRUE)
        }

    ### Previous Version Compatibility
    # Mistakenly, dittoBarPlot used to remove factor identities entirely from the
    #  data it used. This manifests as ignorance of a user's set orderings for
    #  their data. That is nolonger done by default, but to recreate old plots,
    #  restoring this behavior can be achieved with 'retain.factor.levels = FALSE'
    # Set factor level ordering for a metadata we'll give to 'group.by'
    myRNA$groups_reverse_levels <- factor(
        myRNA$groups,
        levels = c("D", "C", "B", "A"))
    # dittoBarPlot will now respect this level order by default.
    dittoBarPlot(myRNA, "clustering", group.by = "groups_reverse_levels")
    # But that respect can be turned off...
    dittoBarPlot(myRNA, "clustering", group.by = "groups_reverse_levels",
        retain.factor.levels = FALSE)

[Package dittoSeq version 1.4.4 Index]