README.md

In khughitt/eda: Exploratory Data Analysis in R

eda - Exploratory Data Analysis for R

The eda package for R provides general purposes, as well as domain-specific classes for performing basic exploratory data analysis in R. It is built on the R6 class system, as well as a number of other powerful statistics, machine learning, and visualization packages.

The primary goals of eda are to provide a simple interface for exploring one or more related datasets, with an emphasis on:

• Quick and easy summary statistics and visualization
• Integration of multiple related datasets
• Streamlined data transformation and visualization using function chaining
• Generalized base classes that can be extended for domain-specific application

This package is still in the early stages of development. While a reasonable overall class hierarchy has been implemented, significant work is still required with respect to normalization of function calls (especially those relating to plotting), and documentation.

Installation

You can install eda using Bioconductor with:

BiocManager::install('github.com/khughitt/eda')

Example Usage

I still need to write a fair bit of documentation for how to actually use this package. That should happen soon (probably Jan 2019).

In the meantime, here are some example use cases to give you a sense for how this package can be used.

The below examples make use of the high-throughput biology (transcriptomic) data made available through the recount2 package.

library(eda)
library(recount)

# download TCGA RNA-Seq data from ReCount
download_study('TCGA')

## Loading eda

# make output reproducible
set.seed(1)

# load TCGA RangedSummarizedExperiment
load(file.path('TCGA', 'rse_gene.Rdata'))

# to speed things up, let's grab a random subsample of the data;
# this can also be done within eda, but there is currently an issue
# relating to transposition of subsampled data, so for now, we will
# handle this externally
SAMPLE_NROWS <- 1000
SAMPLE_NCOLS <- 100

rse_gene <- rse_gene[sample(nrow(rse_gene), SAMPLE_NROWS), sample(ncol(rse_gene), SAMPLE_NCOLS)]

# convert RSE object to an BioDataSet instance
bdat <- BioDataSet$new(rse_gene)

# the expression data and gene / sample metadata are eached stored as
# separate dataset in the BioDataSet object
bdat

## =========================================
## =
## = BioDataSet (n=3)
## =
## =   assays : matrix (1000 x 100)
## =  rowdata : DataFrame (1000 x 3)
## =  coldata : DataFrame (100 x 864)
## =
## =========================================

# each of these can be accessed through the "datasets" property
bdat$datasets$assays[1:3, 1:3]

##                   AEC4FDAA-8F60-43CE-8EBB-5629FA662F16
## ENSG00000211680.2                                    0
## ENSG00000235760.3                                    0
## ENSG00000273129.1                                  904
##                   655B32BE-AC22-4E6C-97D2-CC6B7F06B55E
## ENSG00000211680.2                                    0
## ENSG00000235760.3                                   29
## ENSG00000273129.1                                    0
##                   BDBF3ACE-7DC0-47C1-9B03-E2EDCF0B6CE6
## ENSG00000211680.2                                    0
## ENSG00000235760.3                                  304
## ENSG00000273129.1                                   24

bdat$datasets$coldata[1:3, 1:3]

## DataFrame with 3 rows and 3 columns
##                                          project    sample experiment
##                                      <character> <logical>  <logical>
## AEC4FDAA-8F60-43CE-8EBB-5629FA662F16        TCGA        NA         NA
## 655B32BE-AC22-4E6C-97D2-CC6B7F06B55E        TCGA        NA         NA
## BDBF3ACE-7DC0-47C1-9B03-E2EDCF0B6CE6        TCGA        NA         NA

head(bdat$datasets$rowdata, 3)

## DataFrame with 3 rows and 3 columns
##                             gene_id bp_length          symbol
##                         <character> <integer> <CharacterList>
## ENSG00000211680.2 ENSG00000211680.2        33              NA
## ENSG00000235760.3 ENSG00000235760.3       762      HCG2040054
## ENSG00000273129.1 ENSG00000273129.1       825          PACERR

# subsample data, log-transform, and plot a heatmap
#bdat$subsample(row_n = 500, col_n = 100)$log1p()$plot_heatmap(interactive = FALSE)

# generate a sample PCA, t-SNE, and UMAP plots, colored by cancer 
# TODO: currently an issue with RSE ingestion / handling of colors.. need to look
# into this when I have more time..
#bdat$t()$plot_pca(color_var = 'gdc_cases.project.primary_site', color_key = 'coldata')

khughitt/eda documentation built on May 7, 2019, 10:52 p.m.