Description Usage Arguments Value
Create a scatterplot of a given dimensional reduction set for a Seurat object, coloring and sizing points by the expression level of the chosen feature. Requrires a Seurat object with the reduction to be used in the corresponding object@dr slot
1 2 3 4 5 6 7 | Feature2Plotly3D(object, reduction = "umap", feature_1 = NULL,
feature_2 = NULL, assay_1 = NULL, assay_2 = NULL,
colors_1 = "Reds", colors_2 = "Blues", dim_1 = 1, dim_2 = 2,
dim_3 = 3, bins = 10, return = FALSE, pt_scale = 0.5,
pt_shape = "circle", opacity = 1, plot_height = "750",
plot_width = "750", pt_info = NULL, legend = TRUE,
legend_font_size = 12, plot_grid = FALSE, plot_axes = FALSE)
|
object |
Seurat object |
reduction |
Dimensional reduction to display. Default: 'umap' |
feature_1 |
First feature values to display. Works with anything |
feature_2 |
Second feature values to display. |
assay_1 |
Assay to pull values from for feature_1. Default: NULL |
assay_2 |
Assay to pull values from for feature_2. Default: NULL |
colors_1 |
Colors to use to display values for feature_1. Default: "Reds" |
colors_2 |
Colors to use to display values for feature_2. Default: "Blues" |
dim_1 |
Dimension to display on the x-axis. Default: 1 |
dim_2 |
Dimension to display on the y-axis. Default: 2 |
dim_3 |
Dimension to display on the z-axis. Default: 3 |
bins |
Number of bins to use in dividing expression levels.. Default: 10 |
return |
Return the plot object instead of displaying it. Default: FALSE |
pt_scale |
Factor by which to multiply the size of the points. Default: 5 |
pt_shape |
Shape to use for the points. Default = circle |
opacity |
Transparency level to use for the points, on a 0-1 scale. Default: 1 |
plot_height |
Plot height in pixels. Default: 900 |
plot_width |
Plot width in pixels. Default: 900 |
pt_info |
Meta.data columns to add to the hoverinfo popup.. Default: ident |
legend |
Display legend?. Default: TRUE |
legend_font_size |
Legend font size. Default: 12 |
plot_grid |
Display the major unit tick marks?. Default: FALSE |
plot_axes |
Display the major x, y, and z axes?. Default: FALSE |
If return is TRUE, a plotly object.
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