vignettes/oldvignettefiles/TestingKnit.utf8.md

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

title: "TestingKnit" author: "Wynn Meyer" date: "4/3/2019" output: pdf_document

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

My own work

Attempting to load and plot RER data.

library("RERconverge")
data("toyTrees") 
data("mamRERw")
#repopath = "~/repos"
#source(paste(repopath,"/R/RERfuncs.R",sep=""))
#source(paste(repopath,"/R/plottingFuncs.R",sep="")) #for troubleshooting margins

Here is where I have issues with figure margins.

#plot RERs as tree
#par(mfrow=c(1,1))
newbend3rers = treePlotRers(treesObj=toyTrees, rermat=mamRERw, index="BEND3", 
                            type="c", nlevels=9, figwid=10)

#treePlotRers(treesObj=toyTrees, rermat=mamRERw, index="BEND3", type="c", nlevels=9)

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.