# Data Structure

Here are some tips for using `so` (a spatial object datastructure).

## `SO` Important Features:

- **`so.image_temp()`**
  - Provides the image portion covered by spots.

- **`so.segmentation_final`**
  - Gives the nuclei segmentation plot.

- **`so.pixels_cells`**
  - Represents the final results of cells with the same format as `so.segmentation_final`.

- **`so.final_nuclei`**
  - Stores the nuclei * genes `adata` matrix.

## `SO` Great Results:

- **`adata_sc_final`**
  - `obs`:
    - `cell_cluster`: Denotes the cluster assignment from the iteration.
    - `cos_simularity`: The cosine similarity of the cell's gene expression with the average expression of its cluster.
    - `cell_size`: The number of `2um` spots occupied by this cell.
    - `x` and `y`: The absolute coordinates of the cell, matching the spot locations provided by 10x.
  - `var`:
    - The same as 10x provide for spots*genes array.

##  `SO` Beautiful Visualization:

### 1. `plot_cellcluster_position`

`plot_cellcluster_position(cell_cluster_final, col_num=5)`

This function is often used after `return_celltype_plot` as:

**Example:**

```python
import smurf as su
cell_cluster_final = su.return_celltype_plot(adata_sc, so, cluster_name='leiden')
su.plot_cellcluster_position(cell_cluster_final, col_num=5)
```

It plots the probability of each cell cluster. The first plot will contain all clusters, followed by one plot per cluster.

### 2. `plot_results`

`plot_results(original_image, result_image, transparency=0.6, transparent_background=False, include_label=None, colors=None, dpi=1500, figsize=(20, 20), save=None)`

This function allows you to plot results with the same format as So.segmentation_final mapped onto so.image_temp().

**Parameters:**

- **`original_image`**
  - Normally input `so.image_temp()`.

- **`result_image`**
  - Represents the final results of cells with the same format as `So.segmentation_final`.

- **`transparency`** *(float, optional)*:
  -  The transparency of the result_image. Should be in the range (0, 1].

- **`ransparent_background`** *(bool, optional)*:
  - Whether the zero parts of `result_image` should be transparent.

- **`include_label`** *(bool, optional)*:
  -  Whether to include a label indicating which color refers to which cluster. Useful for cell cluster results and only valid when the number of unique clusters is ≤ 50.

- **`colors`** *(list of tuples, optional)*:
  -  Provide your own colors in the format like`[(255, 0, 0), (0, 255, 0), ...]`. Will use the default colors if `None`.

- **`dpi`** *(int, optional)*:
  - The resolution of the plot. A higher value may decrease speed; a lower value may reduce quality.

- **`figsize`** *(tuple, optional)*:
  - Size of the figure in inches `(width, height)`. Default is `(20, 20)`.

- **`save`** *(str or None, optional)*:
  - The filename to save the plot. If `False` or `None`, the plot will be shown but not saved.

**Example:**

```python
import smurf as su
su.plot_results(so.image_temp(), so.pixels_cells)
```