278 search results for "Heatmap"

How many Authors does the Prime Minister have for his speeches: A Stylometric Analysis

November 17, 2016
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How many Authors does the Prime Minister have for his speeches: A Stylometric Analysis

Some time back, an audio clip was broadcasted on a Pakistani television programme, purportedly of the Prime Minister of Pakistan, Nawaz Sharif, and his aides, who were discussing what to write in an important speech. The clip generated debate for few d...

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Interactive Volcano Plots in R with Plotly

November 16, 2016
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Introduction In a recent blog post, I introduced the new R package, manhattanly, which creates interactive manhattan and Q-Q plots using the plotly.js engine. In the latest CRAN release, you can also create volcano plots. In this post, I describe how to create interactive volcano plots using the manhattanly package. Volcano plots are the negative

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A Free Interactive Plotly R Tutorial

November 9, 2016
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A Free Interactive Plotly R Tutorial

Did you know last month over 23,000 (!) R enthusiasts directly downloaded the Plotly R package? In case you were not one of them, the Plotly package is one of the best R tools to create beautiful, interactive data visualizations as proven by these exa...

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Is ‘Yeah’ Josh and Chuck’s favorite word?

November 5, 2016
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Is ‘Yeah’ Josh and Chuck’s favorite word?

Text mining and sentiment analysis of a Stuff You Should Know Podcast Stuff You Should Know (or SYSK) is one of the many great podcasts from How Stuff Works. The two SYSK hosts Josh and Chuck have taught me so many fascinating things over the years,...

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facet_plot: a general solution to associate data with phylogenetic tree

October 26, 2016
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facet_plot: a general solution to associate data with phylogenetic tree

ggtree provides gheatmap for visualizing heatmap with phylogenetic tree and msaplot for visualizing multiple sequence alignment with phylogenetic tree. We may have different data types and want to visualize and align them with the tree. For example, dotplot of SNP site (e.g. using geom_point(shape='|')), barplot of trait values (e.g. using geom_barh(stat='identity')) et al. To make it easy to associate different...

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[Bioc 34] NEWS of my BioC packages

October 19, 2016
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I have 7 packages published within the Bioconductor project. ChIPseeker clusterProfiler DOSE ggtree GOSemSim meshes ReactomePA A new package meshes was included in BioC 3.4 release. ChIPseeker For ChIPseeker, this release fixed several minor bugs. GEO data was updated, now ChIPseeker contains 20947 bed file information. CHANGES IN VERSION 1.9.8 ------------------------ o plotAvgProf/plotAvgProf2 order of panel by names of input tagMatrix List <2016-09-25, Sun> ...

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reproducible logo generated by ggtree

October 14, 2016
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reproducible logo generated by ggtree

ggtree provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually. Here, as examples, I used ggtree to draw capital character G and C, which are first letter of my name :-). To draw a tree in such shape, we need fan layout (circular layout with open angle) and then rotating the tree...

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Data Scientist with a Wine hobby (Part II)

October 9, 2016
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Data Scientist with a Wine hobby (Part II)

Getting introduced to Google and their API Previously we constructed a data frame that consisted out of the following variables that we might want to perform analysis on: ## "wine_farms" "wine_year" "wine_name" "points" "price" ## ...

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In case you missed it: Septemer 2016 roundup

October 7, 2016
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In case you missed them, here are some articles from September of particular interest to R users. The R-Ladies meetups and the Women in R Taskforce support gender diversity in the R community. Highlights from the Microsoft Data Science Summit include recordings of many presentations about R, and the keynote "The Future of Data Analysis" by Edward Tufte. An...

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Creating an image of a matrix in R using image()

October 6, 2016
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Creating an image of a matrix in R using image()

You have a matrix in R, and you want to visualise it – say, for example, with each cell coloured according to the value in the cell.  Not a heatmap, per se, as that requires clustering; just a simple, visual image. Well, the answer is image() – however, there is the slightly bizarre coding choice

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