Description Usage Arguments Value
Display percentage of cells expressing and levels for a set of features.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | bubbleplot(object, ...)
## S3 method for class 'Seurat'
bubbleplot(
object,
features_plot,
assay = NULL,
slot = "data",
filter_exp_pct = NULL,
filter_apply_method = "any",
filter_apply_group = NULL,
filter_exp_pct_thresh = 0,
filter_exp_level = 0,
avg_func = "mean",
grouping_var = "ident",
x_lab_size = 9,
y_lab_size = 9,
x_axis_title = "Features",
y_axis_title = "Grouping",
pct_legend_title = "Percent group expressing",
scale_legend_title = "Average scaled expression",
x_lab_rot_angle = 45,
preserve_feature_order = FALSE,
cluster_x = TRUE,
cluster_y = FALSE,
colors_use = NULL,
translate_feature_names = FALSE,
annotated_feature_list = FALSE,
do_return = FALSE,
verbose = FALSE,
...
)
|
object |
Seurat object |
... |
ignored |
features_plot |
Either a list of features or a data frame of annotated features to display (see 'annotated_feature_list'). Note: Gene and protein names may be converted to the proper feature name automagically by HGNChelper::checkGeneSymbols if 'translate_feature_names' is TRUE. Features not appearing in the dataset are skipped. |
assay |
Assay to plot. Default: "RNA" |
slot |
Slot to plot. Default: "data" |
filter_exp_pct |
Display only features that are expressed above this fraction. The method by which and groups in which this is judged are controlled by 'filter_apply_method' and 'filter_apply_group', respectively. Default: NULL |
filter_apply_method |
How should 'filter_exp_pct' be applied - should 'any' or 'all' groups be above the desired expression level? Default: "any" |
filter_apply_group |
What identity groups should be considered when applying 'filter_exp_pct? Only works with the active identity or whatever is specified in 'grouping_var'. Default: NULL |
filter_exp_pct_thresh |
Threshold for expression fraction. Default: 0 |
filter_exp_level |
Display only features that are expressed above this level in at least one group. Default: 0 |
avg_func |
Base function to call for measuring average expression. Default: "mean" |
grouping_var |
Variable by which to group cells. Can be cluster identities or any column from the meta.data slot. Default: ident |
x_lab_size |
Font size for the x-axis labels. Default: 9 |
y_lab_size |
Font size for the y-axis labels. Default: 9 |
x_axis_title |
x-axis title |
y_axis_title |
y-axis title |
pct_legend_title |
Percent expressed legend title |
scale_legend_title |
Scale legend title. |
x_lab_rot_angle |
Angle to rotate the x-axis labels. Default: 45° |
preserve_feature_order |
Should the features by displayed in order in which they are given? Overrides cluster_x. Default: FALSE. |
cluster_x |
Arrange the x-axis variables using hierarchical clustering. Default: TRUE |
cluster_y |
Arrange the y-axis variables using hierarchical clustering. Default: FALSE |
colors_use |
Color palette to use to display expression levels. Default: "Reds" |
translate_feature_names |
Should feature names be checked and translated to their correct HUGO Gene Nomenclature Committee name? Default: FALSE |
annotated_feature_list |
Is the feature list annotated? If so, the features will be faceted using their annontations. Requires that 'features_plot' is a two column with the annotations in a column named 'annotations' and features in a column named 'features'. Default: FALSE |
do_return |
Return a ggplot2 object instead of displaying |
verbose |
Show extra output information, like the features that were not found? Default: FALSE |
if isTRUE(do_return), a ggplot2 object
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