Scripts to reproduce the figures from DeepImpute paper

DeepImpute is a single cell RNA-seq imputation algorithm. It is available at https://github.com/lanagarmire/deepimpute

Arisdakessian, Cedric, Olivier Poirion, Breck Yunits, Xun Zhu, and Lana Garmire. "DeepImpute: an accurate, fast and scalable deep neural network method to impute single-cell RNA-Seq data." bioRxiv (2018): 353607" https://www.biorxiv.org/content/early/2018/06/22/353607

Imputing with other methods

The other methods are available in R or python. For the comparison, each imputation results needs to be un-normalized and directly comparable with the initial raw counts.

Pre-requisites

To use these scripts, you need first to:

• Download the datasets:
  • Jurkat, 293T, neuron9k from the 10X genomics platform
  • GSE67602, GSE99330 (Fish_Dropseq), GSE102827 (Hrvatin dataset)
  • The RNA FISH dataset is avaiable at https://www.dropbox.com/sh/g9c84n2torx7nuk/AABZei_vVpcfTUNL7buAp8z-a?dl=0
• Impute all the datasets with all the other 6 methods (or the ones that can be ran)
• Undo normalization if the result is normalized
• Collect all results and organize them the following way:
  • Accuracy experiment: All datasets (jurkat, 293T, neuron9k, GSE67602) are stored in a single h5 file with:
    • One group per dataset
    • For each group, one key per method + 4 other keys (raw for the masked data, truth for unmasked data, cells for cell labels, and genes for gene labels).
  • FISH experiment: Also a single .h5 file. There are 3 groups: dropseq, fish, imputed. The dropseq group consists in the raw dropseq data (raw) + the genes and cells labels. The fish group contains the same information in data, genes and cells. The imputed group has one key per imputation method.
  • Downstram analysis experiment: One .h5ad (scanpy format) per dataset (sim or Hrvatin) per method. The naming is ${method}_${dataset}.h5ad
  • Speed / memory: You will need to setup a google cloud account (detailed specs are in the paper) and setup the instance. A specific docker instance for this experiment is available in the speed_memory folder. For this dataset, you will need to download the Mouse1M dataset from the 10X genomics website and subsample the resulting dataset with the cell numbers specified at the beginning of the wrapper.nf file. Each subsampled dataset must be named mouse1M_{nb_cells}_{transposed,nonTranspoed}.csv, where the files ending with {transposed} have cells as rows and genes as columns, whereas {nonTransposed} corresponds to gene as rows and cells as columns.

Running the scripts

You can run the scripts inside a Docker container. Docker is available at https://www.docker.com/ Once installed, you need to build the container:

# docker build . -t deepimpute_figures

Once built, you can access the container using the following command:

# docker run -v PATH_TO_YOUR_DATA_FOLDER:/workspace/paper_data -it deepimpute_figures

The PATH_TO_YOUR_DATA_FOLDER must be located in the root level of this GitHub folder, and organized the following way:

• The two .h5 files named accuracy.h5 and FISH.h5
• 1 folder downstream with all files with the naming convention {method}_{dataset}.h5ad
• 1 folder speed_memory with the subsampled dataset.

The scripts can then be launched using python script.py or Rscript script.R for R scripts followed by additional flags when needed: For run_accuracy.py and run_downstream_annData.py, you can select the dataset with the "-d" followed by the name (jurkat/293T/GSE67602/neuron9k for the accuracy, and sim/Hrvatin for the downstream analysis). For the speed/memory figure, you just need to run nextflow wrapper.nf

Code

The code is separated into 2 main categories:

• The run_*.py files imputes the data with deepimpute, load the results of other methods (located in paper_data), extract some metrics, and save them in the results folder
• The plot_*{.py,.R} files simply plot the metrics in the results folder.

Some other scripts are available:

• The data masking procedure for the accuracy experiment is in accuracy/data_masking.py
• The simulation parameters are available in the downstream folder