pegasus.violin¶
- pegasus.violin(data, attrs, groupby, hue=None, matkey=None, stripplot=False, inner=None, scale='width', panel_size=(8, 0.5), palette=None, left=0.15, bottom=0.15, wspace=0.1, ylabel=None, return_fig=False, dpi=300.0, **kwargs)[source]¶
Generate a stacked violin plot.
- Parameters
data (
AnnData
orMultimodalData
orUnimodalData
object) – Single-cell expression data.attrs (
str
orList[str]
) – Cell attributes or features to plot. Cell attributes must exist indata.obs
and must be numeric. Features must exist indata.var
.groupby (
str
) – A categorical variable in data.obs that is used to categorize the cells, e.g. Clusters.hue (
str
, optional, default: None) – ‘hue’ should be a categorical variable in data.obs that has only two levels. Set ‘hue’ will show us split violin plots.matkey (
str
, optional, default:None
) – If matkey is set, select matrix with matkey as keyword in the current modality. Only works for MultimodalData or UnimodalData objects.stripplot (
bool
, optional, default:False
) – Attach a stripplot to the violinplot or not. This option will be automatically turn off if ‘hue’ is set.inner (
str
, optional, default:None
) –- Representation of the datapoints in the violin interior:
If
box
, draw a miniature boxplot.If
quartiles
, draw the quartiles of the distribution.If
point
orstick
, show each underlying datapoint.If
None
, will draw unadorned violins.
scale (
str
, optional, default:width
) –- The method used to scale the width of each violin:
If
width
, each violin will have the same width.If
area
, each violin will have the same area.If
count
, the width of the violins will be scaled by the number of observations in that bin.
panel_size (
Tuple[float, float]
, optional, default:(8, 0.5)
) – The size (width, height) in inches of each violin panel.palette (
List[str]
, optional (default:None
)) – Used for setting colors for categories ingroupby
. Within the list, each string is the color for one category.left (
float
, optional, default:0.15
) – This parameter sets the figure’s left margin as a fraction of panel’s width (left * panel_size[0]).bottom (
float
, optional, default:0.15
) – This parameter sets the figure’s bottom margin as a fraction of panel’s height (bottom * panel_size[1]).wspace (
float
, optional, default:0.1
) – This parameter sets the width between panels and also the figure’s right margin as a fraction of panel’s width (wspace * panel_size[0]).ylabel (
str
, optional, default:None
) – Y-axis label. No label to show ifNone
.return_fig (
bool
, optional, default:False
) – Return aFigure
object ifTrue
; returnNone
otherwise.dpi (
float
, optional, default:300.0
) – The resolution in dots per inch.kwargs – Are passed to
seaborn.violinplot
.
- Returns
A
matplotlib.figure.Figure
object containing the dot plot ifshow == False
- Return type
Figure
object
Examples
>>> pg.violin(data, attrs=['CD14', 'TRAC', 'CD34'], groupby='louvain_labels')