README_OLD.md

In caitlinjones/halo: Development version of the package 'halo', which analyzes and visualizes Halo data

Analyze Halo data

This package generates various statistics and plots for Halo data. Currently in its beginning stages, it has been written specifically for melanoma data but as it evolves it ultimately will support all data sets.

Step 1: Install

On MSK server, with R ```{r eval=FALSE} /home/byrne/R/R-3.4.3/bin/R

Run
```{r eval=FALSE}
library(devtools)
install_github("caitlinjones/halo")

Step 2: Create manifest with all project parameters including input files

Example here NOTE: Manifests will soon be built automatically using meta data files, but for now, use template manifests in example/ folder for each step below and modify manually as needed

Step 3 (if applicable): Run ONLY ONE TIME - Mark exclusions

Given raw object analysis *.rda files and exclusion files (including Halo XML, drift summaries and FOV annotations), add an EXCLUDE column to data indicating which cells should not be analyzed. If data has already been marked, skip to Step 4. ```{r eval=FALSE} Rscript scripts/mark_exclusions.R -m example/counts/exclusion_manifest.txt

### Step 3: Run one or more pre-written scripts 

#### * Generate counts of given markers
WARNING: This script has not been tested recently
```{r eval=FALSE}
Rscript scripts/counts.R -m example/counts/counts_manifest.txt

* Spatial Plots

Plot both total density and density by band {r eval=FALSE} Rscript scripts/spatial_plots_2.R -m example/spatial_plots/density_manifest.txt --plotDensity --plotDensityByBand

NOTES: Plotting total density has not been tested since modifying and adding code for plotting density by band Other scripts in scripts/ folder also have not been tested recently * Manifests are a bit painful to create right now - they will soon be built automatically using meta data files and can be modified manually as needed

caitlinjones/halo documentation built on May 7, 2019, 8 a.m.