02_make_figure.r
2015-08-22
Produce a nicer summary figure of sequence and structure clustering.
See ‘01_look_see_download.r’ for data setup and exploratory analysis.
Developed in interactive R mode then rendered with rmarkdown (i.e.)
library(rmarkdown); render("02_make_figure.r")
See sessionInfo() output at end.
# Load required packages
library(bio3d)
library(dendextend)
# Load processed data
load("../data/01_store.RData")
# Figure setup
tanglegram(hc, hc.rmsd, lab.cex=0.6,
main_left ="Sequence Clustering", main_right="Structure Clustering"
, common_subtrees_color_branches=TRUE, lwd=2)
## Lets plot a larger PDF version
pdf("../results/tanglegram_figure.pdf", width=9, height=7)
tanglegram(hc, hc.rmsd, lab.cex=0.6,
main_left ="Sequence Clustering", main_right="Structure Clustering"
, common_subtrees_color_branches=TRUE, lwd=2)
dev.off()
## quartz_off_screen
## 2
# Report on software versions
sessionInfo()
## R version 3.1.2 (2014-10-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] dendextend_1.1.0 bio3d_2.2-2.9000 rmarkdown_0.5.3.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 colorspace_1.2-6 digest_0.6.8 evaluate_0.7
## [5] grid_3.1.2 htmltools_0.2.6 knitr_1.10.5 magrittr_1.5
## [9] parallel_3.1.2 Rcpp_0.11.6 RCurl_1.95-4.6 stringi_0.4-1
## [13] stringr_1.0.0 tools_3.1.2 whisker_0.3-2 XML_3.98-1.2