View source: R/ViolinEnsemble.R
Produce grouped violin plots. Suitable for plotting cluster or cell type specific marker features.
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object |
Seurat object to plot |
features |
List of features to plot |
marker_list |
A table of cluster markers as produced by FindMarkers() or FindAllMarkers or a two column data.frame with the columns "cluster" and "feature". If provided, supercedes the features argument. Note: if a marker is present in multiple clusters, only the first (as determined by arrange()) is used. Default: NULL |
grouping_var |
Grouping variable from ident or meta data to use. If NULL, the current active.ident is used. Default: NULL |
make_features_unique |
For a marker list, keep a feature for only the first cluster it is found it. |
cluster_x |
Arrange the x-axis variables using hierarchical clustering. Default: TRUE |
cluster_y |
Arrange the y-axis variables using hierarchical clustering. Default: FALSE |
show_points |
Display data points in addition to violin using geom_jitter? Default: FALSE |
alpha |
Alpha value to use with geom_jitter. Default: 1 |
pt_size |
Point size to use with geom_jitter. Default: 0.25 |
plot_title |
What it says on the tin. Default: NULL |
assay_use |
Assay to plot. Default: "RNA" |
slot_use |
Slot to draw data from. Default: "data" |
sort |
If TRUE, attempt to sort the groups alpha-numerically. Default: FALSE |
flip |
Should features be displayed along the y-axis? Default: TRUE |
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