Plotting

picturedrocks.plot.genericplot(celldata, coords, **scatterkwargs)

Generate a figure for some embedding of data

This function supports both 2D and 3D plots. This may be used to plot data for any embedding (e.g., PCA or t-SNE). For example usage, see code for pcafigure.

Parameters:
  • celldata (anndata.AnnData) – data to plot
  • coords (numpy.ndarray) – (N, 2) or (N, 3) shaped coordinates of the embedded data
  • **scatterkwargs – keyword arguments to pass to Scatter or Scatter3D in plotly (dictionaries are merged recursively)
picturedrocks.plot.genericwrongplot(celldata, coords, yhat, labels=None, **scatterkwargs)

Plot figure with incorrectly classified points highlighted

This can be used with any 2D or 3D embedding (e.g., PCA or t-SNE). For example code, see pcawrongplot.

Parameters:
  • celldata (anndata.AnnData) – data to plot
  • coords (numpy.ndarray) – (N, 2) or (N, 3) shaped array with coordinates to plot
  • yhat (numpy.ndarray) – (N, 1) shaped array of predicted y values
  • labels (list, optional) – list of axis titles
  • **scatterkwargs – keyword arguments to pass to Scatter or Scatter3D in plotly (dictionaries are merged recursively)
picturedrocks.plot.pcafigure(celldata, **scatterkwargs)

Make a 3D PCA figure for an AnnData object

Parameters:
  • celldata (anndata.AnnData) – data to plot
  • **scatterkwargs – keyword arguments to pass to Scatter or Scatter3D in plotly (dictionaries are merged recursively)
picturedrocks.plot.pcawrongplot(celldata, yhat, **scatterkwargs)

Generate a 3D PCA figure with incorrectly classified points highlighted

Parameters:
  • celldata (anndata.AnnData) – data to plot
  • yhat (numpy.ndarray) – (N, 1) shaped array of predicted y values
  • **scatterkwargs – keyword arguments to pass to Scatter or Scatter3D in plotly (dictionaries are merged recursively)
picturedrocks.plot.plotgeneheat(celldata, coords, genes, hide_clusts=False, **scatterkwargs)

Generate gene heat plot for some embedding of AnnData

This generates a figure with multiple dropdown options. The first option is “Clust” for a plot similar to genericplot, and the remaining dropdown options correspond to genes specified in genes. When celldata.genes is defined, these drop downs are labeled with the gene names.

Parameters:
  • celldata (anndata.AnnData) – data to plot
  • coords (numpy.ndarray) – (N, 2) or (N, 3) shaped coordinates of the embedded data (e.g., PCA or tSNE)
  • genes (list) – list of gene indices or gene names
  • hide_clusts (bool) – Determines if cluster labels are ignored even if they are available
picturedrocks.plot.umapfigure(adata, **scatterkwargs)