Single-cell plot
Function to visualize coordinate representation of individual cells:
- bigfish.plot.plot_cell(ndim, cell_coord=None, nuc_coord=None, rna_coord=None, foci_coord=None, other_coord=None, image=None, cell_mask=None, nuc_mask=None, boundary_size=1, title=None, remove_frame=True, rescale=False, contrast=False, framesize=(15, 10), path_output=None, ext='png', show=True)
Plot image and coordinates extracted for a specific cell.
- Parameters:
- ndim{2, 3}
Number of spatial dimensions to consider in the coordinates.
- cell_coordnp.ndarray, optional
Coordinates of the cell border with shape (nb_points, 2). If None, coordinate representation of the cell is not shown.
- nuc_coordnp.ndarray, optional
Coordinates of the nucleus border with shape (nb_points, 2).
- rna_coordnp.ndarray, optional
Coordinates of the detected spots with shape (nb_spots, 4) or (nb_spots, 3). One coordinate per dimension (zyx or yx dimensions) plus the index of the cluster assigned to the spot. If no cluster was assigned, value is -1. If only coordinates of spatial dimensions are available, only centroid of foci can be shown.
- foci_coordnp.ndarray, optional
Array with shape (nb_foci, 5) or (nb_foci, 4). One coordinate per dimension for the foci centroid (zyx or yx dimensions), the number of spots detected in the foci and its index.
- other_coordnp.ndarray, optional
Coordinates of the detected elements with shape (nb_elements, 3) or (nb_elements, 2). One coordinate per dimension (zyx or yx dimensions).
- imagenp.ndarray, optional
Original image of the cell with shape (y, x). If None, original image of the cell is not shown.
- cell_masknp.ndarray, optional
Mask of the cell.
- nuc_masknp.ndarray, optional
Mask of the nucleus.
- boundary_sizeint, default=1
Width of the cell and nucleus boundaries, in pixel.
- titlestr, optional
Title of the image.
- remove_framebool, default=True
Remove axes and frame.
- rescalebool, default=False
Rescale pixel values of the image (made by default in matplotlib).
- contrastbool, default=False
Contrast image.
- framesizetuple, default=(15, 10)
Size of the frame used to plot with
plt.figure(figsize=framesize).- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.
- bigfish.plot.plot_cell_coordinates(ndim, cell_coord, nuc_coord, rna_coord, titles=None, remove_frame=True, framesize=(10, 5), path_output=None, ext='png', show=True)
Plot cell coordinates for one or several cells.
- Parameters:
- ndim{2, 3}
Number of spatial dimensions to consider in the coordinates.
- cell_coordnp.ndarray or list
Coordinates or list of coordinates of the cell border with shape (nb_points, 2).
- nuc_coordnp.ndarray or list
Coordinates or list of coordinates of the nucleus border with shape (nb_points, 2).
- rna_coordnp.ndarray or list
Coordinates or list of coordinates of the detected spots with shape (nb_spots, 3) or (nb_spots, 2). One coordinate per dimension (zyx or yx dimensions).
- titlesstr or list, optional
Title or list of titles.
- remove_framebool, default=True
Remove axes and frame.
- framesizetuple, default=(10, 5)
Size of the frame.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.