simba.pl.query
- simba.pl.query(adata, comp1=1, comp2=2, obsm='X_umap', layer=None, color=None, dict_palette=None, size=8, drawing_order='random', dict_drawing_order=None, show_texts=False, texts=None, text_expand=(1.05, 1.2), text_size=10, n_texts=8, fig_size=None, fig_ncol=3, fig_legend_ncol=1, fig_legend_order=None, alpha=0.9, alpha_bg=0.3, pad=1.08, w_pad=None, h_pad=None, save_fig=None, fig_path=None, fig_name='plot_query.pdf', vmin=None, vmax=None, **kwargs)[source]
Plot query output
- Parameters:
adata (Anndata) – Annotated data matrix.
comp1 (int, optional (default: 1)) – Component used for x axis.
comp2 (int, optional (default: 2)) – Component used for y axis.
obsm (str, optional (default: ‘X_umap’)) – The field to use for plotting
layer (str, optional (default: None)) – The layer to use for plotting
color (list, optional (default: None)) – A list of variables that will produce points with different colors. e.g. color = [‘anno1’, ‘anno2’]
dict_palette (dict,optional (default: None)) – A dictionary of palettes for different variables in color. Only valid for categorical/string variables e.g. dict_palette = {‘ann1’: {},’ann2’: {}}
size (int (default: 8)) – Point size.
drawing_order (str (default: ‘random’)) –
The order in which values are plotted, This can be one of the following values
’original’: plot points in the same order as in input dataframe
’sorted’ : plot points with higher values on top.
’random’ : plot points in a random order
dict_drawing_order (dict,optional (default: None)) – A dictionary of drawing_order for different variables in color. Only valid for categorical/string variables e.g. dict_drawing_order = {‘ann1’: ‘original’,’ann2’: ‘sorted’}
show_texts (bool, optional (default: False)) – If True, text annotation will be shown.
text_size (int, optional (default: 10)) – The text size.
texts (list optional (default: None)) – Point names to plot.
text_expand (tuple, optional (default: (1.05, 1.2))) – Two multipliers (x, y) by which to expand the bounding box of texts when repelling them from each other/points/other objects.
n_texts (int, optional (default: 8)) – The number of texts to plot.
fig_size (tuple, optional (default: (4, 4))) – figure size.
fig_ncol (int, optional (default: 3)) – the number of columns of the figure panel
fig_legend_order (dict,optional (default: None)) – Specified order for the appearance of the annotation keys. Only valid for categorical/string variable e.g. fig_legend_order = {‘ann1’:[‘a’,’b’,’c’],’ann2’:[‘aa’,’bb’,’cc’]}
fig_legend_ncol (int, optional (default: 1)) – The number of columns that the legend has.
vmin (float, optional (default: None)) – The min and max values are used to normalize continuous values. If None, the respective min and max of continuous values is used.
vmax (float, optional (default: None)) – The min and max values are used to normalize continuous values. If None, the respective min and max of continuous values is used.
alpha (float, optional (default: 0.9)) – The alpha blending value, between 0 (transparent) and 1 (opaque) for returned points.
alpha_bg (float, optional (default: 0.3)) – The alpha blending value, between 0 (transparent) and 1 (opaque) for background points
pad (float, optional (default: 1.08)) – Padding between the figure edge and the edges of subplots, as a fraction of the font size.
h_pad (float, optional (default: None)) – Padding (height/width) between edges of adjacent subplots, as a fraction of the font size. Defaults to pad.
w_pad (float, optional (default: None)) – Padding (height/width) between edges of adjacent subplots, as a fraction of the font size. Defaults to pad.
save_fig (bool, optional (default: False)) – if True,save the figure.
fig_path (str, optional (default: None)) – If save_fig is True, specify figure path.
fig_name (str, optional (default: ‘plot_query.pdf’)) – if save_fig is True, specify figure name.
- Return type:
None