Fast data portals for scRNAseq data

This repository contains tools for making web portals and interactive tools used for exploring and visualising single cell RNA data.

Interactive tools and web portals:

web_portal.sh

• see an example here
• the pipeline can be called with web_portal.sh
• this take as input an option file
• option files should be placed in the options folder
• inside this folder there are two examples: one option file for a seurat object (liver_web_portal_options.txt) and on option file for scanpy objects (thymus_web_portal_options.txt)
• the format of the option file:
  • line 1 indicates data file: "file_name: ../../data/mydata.RDS"
  • line 2 indicates output folder: "output_folder: output_here/my_dear_web_portal"
  • line 3 indicates what dimenssionality reduction types to be included: "dr_coordonates: UMAP->X_umap; tSNE->X_tsne; FDG->X_draw_graph_fa;". Each field must end with ";". The dr fields must be in the @dr slot for seurat objects or in data.obsm[dr_coor] attribute for scanpy objects.
  • line 4 indicates meta data fields to include in the portal: "Cell Labels->Annotation->null;Flow gate->sort->null;Sample->fetus->null;Gender->gender->null;". Each field must end with ";". Each field indicate the name of the meta data column followed by "->" followed by name of the field to appear in the data portal (for example you might have a meta data column called "sort.ids" but on the web portal you want it to appear as "Sorting gates") followed by "->" followed by the name color key (csv file found in the resource folder) or set to "null" ir such a color key does not exist for a particular meta data and random colours must be generated instead.
• the output is tar.gz file. Unziping this will generate a folder with lots of contents (the web portal folder)
• if you require password protection go to the folder templates_password_protection and run the Python script generate_password.py. This will insert a new password to the template. The password is written to the file password.txt. Keep this for reference.
• copy paste to web portal folder the 4 files from the folder templates_password_protection (if you need password protection) or from folder folder templates_no_password_protection (if you do not need password protection)
• these files are: fetch_category.php, fetch_dr_coordinates.php, fetch_gene_expression.php, index.php
• upload to web server

interactive_heatmap_dotplot.sh

• see an example here
• this is used to generated an interactive heatmap/dot plot from a seurat object or scanpy object
• takes one argument which is the path of an option files
• there are two examples of option files in the folder options: options_fetal_liver.txt for a seurat object and options_fetal_thymus.txt for a scanpy object
• format of the option file:
  • line 1: data file path
  • line 2: meta data column by which to assign the identity of cells
  • line 3: name of output folder
  • line 4: name of interactive html page
  • line 5: a short line describing the data which will be included in the interactive page
• IMPORTANT NOTICE: if the vector partitioning the data (i.e. meta data column) is using integer indices (e.g. Louvain clustering which assigns integer identifies to clusters) it is highly recommended to pre-append the tag "Cluster_" to all indices (e.g. "1" and "103" becomes "Cluster_1" and "Cluster_103" respectively). Failure to do so will not raise any errors, but the resulting interactive heatmap/dot plot will have glitches.

pseudotime_webportal.sh

• see an example here
• this creates a web portal useful for exploring the results of a trajectory analysis
• this only works on seurat objects, and not on scanpy objects
  • seurat.addr full or relative path of the file storing the seurat object or scanpy object
  • set.ident meta data column used for partion the data
  • cell.types an R character vector listing the cell types to used in the trajectory. White spaces in the names must be replaced with double at sign ("@@").
  • root_cell_type name of the cell type to use as root
  • type.to.colours full or relative path to the color key (a csv file mapping cell types to colours). To generate your own colour key use color_management.html (see here)
  • lineage.name lineage name that appears in the portal. White spaces must be replaced with double at sign ("@@" instead of " ")

gene_grouping.sh

• creates a graphical interface for fast data exploration of gene expression.
• the resulting program also groups genes by expression patterns and allows the user to manually change group assignment
  • seurat.addr full or relative path of the file storing the seurat object
  • no_clusters number of gene clusters required
• the output is a folder
• copy the gene_viewer.py script to the outputted folder and then you can run the GUI from a python shell