dynamo.pl.space

dynamo.pl.space(adata, color=None, genes=[], gene_cmaps=None, space_key='spatial', width=6, marker='.', pointsize=None, dpi=100, ps_sample_num=1000, alpha=0.8, stack_genes=False, stack_genes_threshold=0.01, stack_colors_legend_size=10, figsize=None, *args, **kwargs)[source]

Scatter plot for physical coordinates of each cell.

Parameters
  • adata (AnnData) – an Annodata object that contain the physical coordinates for each bin/cell, etc.

  • genes (Optional[list]) – The gene list that will be used to plot the gene expression on the same scatter plot. Each gene will have a different color. Can be a single gene name string and we will convert it to a list.

  • gene_cmaps – A list of cmaps for mapping each gene’s values according to a type of cmap when stacking gene colors on the same subplot. The order of each gene’s cmap corresponds to the order in genes.

  • color (string (default: ntr)) – Any or any list of column names or gene names, etc. that will be used for coloring cells. If color is not None, stack_genes will be disabled automatically because color can contain non numerical values.

  • space_key (str) – The key to space coordinates.

  • stack_genes (bool) – whether to show all gene plots on the same plot

  • stack_genes_threshold (float) – lower bound of gene values that will be drawn on the plot.

  • stack_colors_legend_size (int) – control the size of legend when stacking genes

  • alpha (float) – The alpha value of the scatter points.

  • width (int) –

  • marker (str) – a string representing some marker from matplotlib https://matplotlib.org/stable/api/markers_api.html#module-matplotlib.markers

  • pointsize (float) – The size of the points on the scatter plot.

  • dpi (float, (default: 100.0)) – The resolution of the figure in dots-per-inch. Dots per inches (dpi) determines how many pixels the figure comprises. dpi is different from ppi or points per inches. Note that most elements like lines, markers, texts have a size given in points so you can convert the points to inches. Matplotlib figures use Points per inch (ppi) of 72. A line with thickness 1 point will be 1./72. inch wide. A text with fontsize 12 points will be 12./72. inch heigh. Of course if you change the figure size in inches, points will not change, so a larger figure in inches still has the same size of the elements.Changing the figure size is thus like taking a piece of paper of a different size. Doing so, would of course not change the width of the line drawn with the same pen. On the other hand, changing the dpi scales those elements. At 72 dpi, a line of 1 point size is one pixel strong. At 144 dpi, this line is 2 pixels strong. A larger dpi will therefore act like a magnifying glass. All elements are scaled by the magnifying power of the lens. see more details at answer 2 by @ImportanceOfBeingErnest: https://stackoverflow.com/questions/47633546/relationship-between-dpi-and-figure-size

  • ps_sample_num (int) – The number of bins / cells that will be sampled to estimate the distance between different bin / cells.

Return type

plots gene or cell feature of the adata object on the physical spatial coordinates.