Publications by Shirin's playgRound
How to set up your own R blog with Github pages and Jekyll Bootstrap
This post is in reply to a request: How did I set up this R blog? I have wanted to have my own R blog for a while before I actually went ahead and realised this page. I had seen all the cool things people do with R by following R-bloggers and reading their newsletter every day! While I am using R every day at work, the thematic scope there is of ...
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Creating a network of human gene homology with R and D3 (without html widget for easy loading)
The html widget I produced with networksD3 seems to create problems with loading the site for some people, so here is the same blog post as yesterday just without the rendered html widget in it. This week I want to explore how many of our human genes have homologs in other species. I will use this question to show how to visualize dendrograms an...
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Gene homology Part 2 – creating directed networks with igraph
In my last post I created a gene homology network for human genes. In this post I want to extend the network to include edges for other species. First, I am loading biomaRt and extract a list of all available datasets. library(biomaRt) ensembl = useMart("ensembl") datasets <- listDatasets(ensembl) For this network I don’t want to include all s...
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How to build a Shiny app for disease- & trait-associated locations of the human genome
This app is based on the gwascat R package and its ebicat38 database and shows trait-associated SNP locations of the human genome. You can visualize and compare the genomic locations of up to 8 traits simultaneously. The National Human Genome Research Institute (NHGRI) catalog of Genome-Wide Association Studies (GWAS) is a curated resource of sin...
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Animating Plots of Beer Ingredients and Sin Taxes over Time
With the upcoming holidays, I thought it fitting to finally explore the ttbbeer package. It contains data on beer ingredients used in US breweries from 2006 to 2015 and on the (sin) tax rates for beer, champagne, distilled spirits, wine and various tobacco items since 1862. I will be exploring these datasets and create animated plots with the ani...
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How to map your Google location history with R
It’s no secret that Google Big Brothers most of us. But at least they allow us to access quite a lot of the data they have collected on us. Among this is the Google location history. If you want to see a few ways how to quickly and easily visualize your location history with R, stay tuned… The Google location history can be downloaded from yo...
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Gene homology Part 3 – Visualizing Gene Ontology of Conserved Genes
Which genes have homologs in many species? In Part 1 and Part 2 I have already explored gene homology between humans and other species. But there I have only considered how many genes where shared between the species. In this post I want to have a closer look at genes with homologs in many species. These genes are likely evolutionarily convserved...
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Feature Selection in Machine Learning (Breast Cancer Datasets)
Machine learning uses so called features (i.e. variables or attributes) to generate predictive models. Using a suitable combination of features is essential for obtaining high precision and accuracy. Because too many (unspecific) features pose the problem of overfitting the model, we generally want to restrict the features in our models to those,...
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R vs Python – a One-on-One Comparison
I’m an avid R user and rarely use anything else for data analysis and visualisations. But while R is my go-to, in some cases, Python might actually be a better alternative. That’s why I wanted to see how R and Python fare in a one-on-one comparison of an analysis that’s representative of what I would typically work with. Conclusions All in ...
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Exploring World Gender Statistics with Shiny
This week I explored the World Gender Statistics dataset. You can look at 160 measurements over 56 years with my Shiny app here. I prepared the data as follows: Data.csv Country.Name: the name of the country Country.Code: the country’s code Indicator.Name: the name of the variable that this row represents Indicator.Code: a unique id for the v...
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