BubblePlotly: BubblePlotly
In milescsmith/SeuratPlotly: Plotly-based methods for displaying Seurat data

Description Usage Arguments

Plot average expression levels and proportion expressing a feature arranged by given grouping_var. Color intensity of the markers indicates expression levels and size of the marker indicates the proportion of the group expressing the feature above a given threshold. By default, features are arranged along the x-axis and groups along the y-axis.

BubblePlotly(object, features_plot, assay = NULL, slot = "data",
  grouping_var = "ident", colors = "Blues", dot_min = 0,
  dot_scale = 2, plot_legend = FALSE, return = FALSE,
  x_label_rotation = -45, plot_width = 600, plot_height = 600,
  x_font_size = 10, y_font_size = 10, title_font_size = 12,
  legend_text_size = 10, opacity = 1, plot_title = NULL, bins = 50,
  flip = FALSE, alphabetize = TRUE, pct_expr_thres = NULL,
  show_zeros = FALSE, add_group = NULL, y_label_order = NULL)

`object`	Seurat object
`features_plot`	Features to display values for. If trying to retrieve values from an assay that is not the current DefaultAssay, prefix the feature name with 'assay_'. Works with anything `Seurat::FetchData` can retrieve.
`assay`	Assay to pull data from. Defaults to the object's DefaultAssay
`slot`	Slot to pull data from. Default: 'data'
`grouping_var`	Factor by which to group cells. Default: ident
`colors`	Color palette to use. Default: Reds
`dot_min`	Minimium marker size, in pixels. Default: 0
`dot_scale`	Factor by which to scale markers. Default: 2
`plot_legend`	Display legend? Default: FALSE
`return`	Return the generated data frame underlying the graph. Default: FALSE
`x_label_rotation`	Angle by which to rotate the x-axis labels, in degrees relative to horizontally aligned text. Default -45°
`plot_width`	Plot width in pixels. Default: 900
`plot_height`	Plot height in pixels. Default: 900
`x_font_size`	Size of the x-axis titles. Default: 10
`y_font_size`	Size of the y-axis titles. Default: 10
`title_font_size`	Size of the plot title. Default: 12
`legend_text_size`	Size of the legend text. Default: 10
`opacity`	Transparency level to use for the points, on a 0-1 scale Default: 1
`plot_title`	Display title with the name of the feature? Default TRUE
`bins`	Number of bins to use in dividing expression levels. Default: 10
`flip`	Swap the x- and y-axes so that features are on the y-axis and groups along the x-axis. Default: false
`alphabetize`	Alphabetize the display order of features Default: TRUE
`pct_expr_thres`	Hide a feature if there is no group that expresses at or above this percentage. Default: 0
`show_zeros`	Display comparison groups for which there there was no data? Default: FALSE
`add_group`	Add a null comparison group. Will be initialized with zeros.
`y_label_order`	List of labels to use for the comparison groups. Will be displayed in order of their index.