stereo.plots.PlotCollection.gaussian_smooth_scatter_by_gene#
- PlotCollection.gaussian_smooth_scatter_by_gene(gene_name=None, dot_size=None, palette='CET_L4', color_bar_reverse=True, width=None, height=None, x_label=['spatial1', 'spatial1'], y_label=['spatial2', 'spatial2'], title=None, vmin=None, vmax=None, **kwargs)[source]#
Draw the spatial distribution of expression quantity of the gene specified by gene names, just only for Gaussian smoothing, inluding the raw and smoothed.
- Parameters:
gene_name (
Optional
[str
]) – specify the gene you want to draw, ifNone
by default, will select randomly.dot_size (
Optional
[int
]) – marker sizemarker size, defaults toNone
.palette (
Optional
[str
]) – Color theme, defaults to'CET_L4'
.color_bar_reverse (
Optional
[bool
]) – if True, reverse the color bar, defaults to Falsewidth (
Optional
[int
]) – the figure width in pixels.height (
Optional
[int
]) – the figure height in pixels.x_label (
Optional
[list
]) – list of x label.y_label (
Optional
[list
]) – list of y label.title (
Optional
[list
]) – list of title label(lists of size two).show_plotting_scale – wheter to display the plotting scale.
out_path – the path to save the figure.
out_dpi – the dpi when the figure is saved.
reorganize_coordinate –
if the data is merged from several slices, whether to reorganize the coordinates of the obs(cells), if set it to a number, like 2, the coordinates will be reorganized to 2 columns on coordinate system as below:
data1 data2data3 data4data5 …… …if set it to
False
, the coordinates will not be changed.horizontal_offset_additional – the additional offset between each slice on horizontal direction while reorganizing coordinates.
vertical_offset_additional – the additional offset between each slice on vertical direction while reorganizing coordinates.
vmin (
Optional
[float
]) – The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.vmax (
Optional
[float
]) – The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.