cellmanager

A Package for managing cell type about color and markers while processing scRNA-seq data.

Installation

It's easy to install cellmanager via pip!

pip install cellmanager

Basic usage

1. First, the user should prepare a TOML file as below.

   [Immnue]
   
   [Immnue.Lyphoid]
   
   [Immnue.Lyphoid.T]
   color = "#1ba169"
   markers = ["CD3D", "CD3E", "CD3G", "CD8A", "TRBC2"]
   
   [Immnue.Lyphoid.T."CD8+ T"]
   markers = ["CD8A", "CD8B"]
   
   [Immnue.Lyphoid.T."CD4+ T"]
   markers = ["CD40LG", "FOXP3", "CD4"]
   
   [Immnue.Lyphoid.NK]
   color = "#014431"
   markers = ["GNLY", "NKG7", "FGFBP2", "FCGR3A", "CX3CR1", "KLRB1", "NCR1"]

   Let me explain the basic logic of the data structure in the TOML file:

   • Top-level category (like [Immune] in the example above): The top-level category is indicated with square brackets []. In this case, [Immune] defines the main section of the file, grouping all immune-related data.

   • Nested subcategories [Immune.Lyphoid]: You can create nested sections by using dot notation (e.g., Lyphoid under Immune). This creates a hierarchical structure to organize related data within the top-level category.

   • Further sub-nesting [Immune.Lyphoid.T]: Further subcategories can be defined by continuing to nest sections using dots. For example, [Immune.Lyphoid.T] indicates a further refinement under Lyphoid.

   • Attributes: Inside each section, key-value pairs define attributes.

     For most usage cases, color and markers are used frequently.

     color = "#1ba169" assigns a color attribute, and markers = [...] defines a list of markers.

   [!TIP]

   We have designed the # character as a placeholder to keep the hierarchy consistent. We will introduce this below, so don't worry.

2. Create a CellManager object

   from cellmanager import CellManager
   
   manager = CellManager("data.toml") # Input your TOML file path here.

3. Visualize your cell-type view

   # tree 
   manager.render_tree()
   
   # level group
   
   manager.render_lavel_table()

   

   [!NOTE]

   The # character is used as a placeholder to keep related cell types at the same level.

4. Visualize the markers of cell-type

   # markers of all cell type
   manager.render_markers_table()
   
   # markers of specific cell type
   manager.render_markers_table(cluster="Endothelial")

   

   

5. Query information

   • by and key are the two most important parameters in CellManager.query()function.

   • info control to output color or markers, default markers

   • output_format control to output as dict or list, default dict.

   We provide three query methods:

   1. Query by cluster

      by = "cluster"

      key = Which cluster do you want to know (like "T" as below)

      include_major is a bool parameter controlling whether to output the major cell type.

      Example:

      

   2. Query by level

      [!WARNING]

      If you want to query by level, you must first run the CellManager.render_level_table()function to ensure that the user confirms the level information

      by = "level"

      key = Which level do you want to know

      Example:

      As shown above, there are eight cell types in the level 3.

      

      

   3. Query by a custom list

      Also, if you want to query a custom list you are interested in, you can use this method

      by = "list"

      key = [...] everything you want to query