Computational biology and genomics
ARCHS4 (All RNA-seq and ChIP-seq sample and signature search) is a resource that provides access to gene and transcript counts uniformly processed (using kallisto) from all human and mouse RNA-seq experiments from the Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA). The tool gget and the sub-tool archs4 can be used to query…
The grImport package can be used to import vector images into R so that you can edit and/or combine it other plots. In this post, I will go through the grImport workflow and finally show how vector images can be incorporated with other graphical objects.
I haven’t been blogging as much as I’d like to due to other commitments but I wanted to write a post before 2018 ends. This post is on plotting Google Trends results with R. If you’ve never heard of or used Google Trends, it’s fun! You can see how certain keywords have trended over the…
Interactive plots, as the name suggests, are plots that users can interact with. In my last post, I mentioned that for interactive heatmaps I use the d3heatmap package. To get started with this post, I’ll create the same heatmap as my last post but this time using the d3heatmap package.
For a while, heatmap.2() from the gplots package was my function of choice for creating heatmaps in R. Then I discovered the superheat package, which attracted me because of the side plots. However, shortly afterwards I discovered pheatmap and I have been mainly using it for all my heatmaps (except when I need to interact…
The diagram package makes it easy to create flowcharts in R. In this post I’ll show an example of creating a simple flowchart. The most important part is to understand how the coordinate systems works; once you understand that, it’s just a matter of placing your arrows and boxes accordingly to create your flowchart. To…
An adjacency list is simply an unordered list that describes connections between vertices. It’s a commonly used input format for graphs. In this post, I use the melt() function from the reshape2 package to create an adjacency list from a correlation matrix. I use the geneData dataset, which consists of real but anonymised microarray expression…
I discovered the superheat package a few days ago and the adjacent plots feature was really attractive. The superheat #rstats package for making heatmaps looks super! I like the adjacent plots https://t.co/KhyA6K6Ap3 — Dave Tang (@davetang31) February 3, 2017
I found out about plotly a couple of months ago via R-bloggers: Gantt charts in R using Plotly via @Rbloggers #rstats https://t.co/LuW8nuQr6c — Dave Tang (@davetang31) May 13, 2016 I finally gave it a go when a friend asked me for help making a Gantt chart and I was impressed with plotly’s interactivity and ease…
At the start of this year I created a Twitter account that automatically tweets out papers related to transcriptomes, i.e. a Twitter literature bot. This idea isn’t new and there are over 200 Twitter literature bots. However, I wrote my Twitter bot using R (and using the RISmed package to search PubMed for papers) and…