15 January 2014

knitcitations, pander, and pandoc

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Wednesday notes

Comments on Grace’s undergrad research proposal.

Catching up on literature.


Bioanalyzer results are NIL for all samples. Probably shouldn’t have diluted. If Nanodrop overestimates, the samples were already in the Pico range before diluting.

Update table


Started new tech report “ApTranscriptome_TR.Rmd” that details Aphaenogaster transcriptome assembly and analysis of thermally-responsive genes. This tech report details the commands to generate the transcriptome, but does not aim to be completely reproducible as my previous script (“ApTran_assemble.R”) because it was just too damn difficult. Instead, I include downloading the transcriptome assembly, annotaiton and expression value matrices. Only the identification of responsive genes is fully reproducible.


Installed knitcitations on workstation. Required first installing devtools which required RCurl which itself required a system install of curl sudo apt-get install libcurl4-gnutls-dev following this guide. Also had to install XML with sudo apt-get install libxml2-dev so I could install the CRAN version of ‘knitcitations’. Yikes!

To download files from web within R to local directory, use downloadFile() from the R.utils package.


Also used pander library to create pandoc style tables. MUCH easier than trying to do these myself. Need to automate markdown –> knitr –> pandoc –> jekyll so I can start using this to create table. For example:

```{r assemstats, results = "asis", echo=FALSE}
# make table
trinity <- c("126,172", "100,389,539", "358", "795", "16,201", "1,631")
reduced <- c("105,536", "62,648,997", "320", "593", "15,491", "895")

assemstats <- rbind(trinity, reduced)
colnames(assemstats) <- c("Total contigs", "Total length", "Median contig size", "Mean contig size", "N50 contig", "N50 Length")

pandoc.table(assemstats, style="rmarkdown", caption = "Table 1: Statistics for Trinity and cap3+uclust reduced transcriptome assemblies")

Generates this nice table after knitr:

|    &nbsp;     |  Total contigs  |  Total length  |  Median contig size  |
|  **trinity**  |     126,172     |  100,389,539   |         358          |
|  **reduced**  |     105,536     |   62,648,997   |         320          |

Table: Table 1: Statistics for Trinity and cap3+uclust reduced transcriptome assemblies (continued below)


|    &nbsp;     |  Mean contig size  |  N50 contig  |  N50 Length  |
|  **trinity**  |        795         |    16,201    |    1,631     |
|  **reduced**  |        593         |    15,491    |     895      |

which generates nicely in html through pandoc.

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