Better formatting for PDF knitting

.Rhistory

-names(colors_genera_pp) <- genera_pp
-colors_genera_other <- viridis(length(genera_other), option = "D", begin = 1 ,end = 0.9)
-names(colors_genera_other) <- genera_other
-colors_oomyc_genera <- c(colors_genera_pp, colors_genera_other)
-#Sort alphabetically by vector names to avoid mixing up color assignments (origin of issue not resolved)
-colors_oomyc_genera <- colors_oomyc_genera[order(names(colors_oomyc_genera))]
-colors_oomyc_genera["Phytophthora"] <- viridis_reds[1]
-colors_oomyc_genera["Pythium"] <- viridis_reds[4]
-shared_theme <- theme(legend.key.size = unit(3, "mm"), legend.position = "none", axis.title.x = element_blank(), plot.margin = margin(20,10,10,10), legend.text.align = 0)
-shared_theme_abu <- theme(legend.key.size = unit(3, "mm"), legend.position = "none", axis.title.x = element_blank(),  plot.margin = margin(20,10,10,10),legend.text.align = 0)
-if(customLabels){
-labelling <- c(expression(paste("uncultured ", italic("Apodachlya"))),
-expression(paste("uncultured ", italic("Lagenidium"))),
-expression(paste("uncultured ", italic("Oomycetes"))),
-expression(paste("uncultured ", italic("Phytophthora"))),
-expression(paste("uncultured ", italic("Pythium"))),
-expression(italic("Achlya"), italic("Albugo"), italic("Aphanomyces"),
-italic("Apodachlya"), italic("Atkinsiella"), italic("Bremia"),
-italic("Brevilegnia"), italic("Dictyuchus"), italic("Eurychasma"),
-italic("Geolegnia"), italic("Globisporangium"), italic("Halocrusticida"),
-italic("Haptoglossa"), italic("Hyaloperonospora"), italic("Lagena"),
 italic("Lagenidium"), italic("Leptolegnia"), italic("Myzocytiopsis"),
 italic("Paralagenidium"), italic("Peronospora"), italic("Phragmosporangium"),
 italic("Phytophthora"), italic("Phytopythium"), italic("Pilasporangium"),
@@ -510,3 +489,24 @@ cat(topnt_summary, "\n\n", topnt2_summary)
 cat(prctg_pyth_phyt_str)
 combobar1
 cat("Chunk successfully run")
+# CHANGE ME according to the location containing 'seqtab_nochim.rds' and other relevant files.
+path = "Data_files/"
+# CHANGE ME to 'TRUE' to list all samples and generate an empty metadata file
+optional_sample_check <- "FALSE"
+# CHANGE ME to TRUE to update the cuphyr package. This is a package the author published to separate out general purpose functions from this script. If the package is not installed, it will be installed, regardless of the value chosen here.
+update_cuphyr <- TRUE
+################# NO CHANGES NECESSARY BELOW #################
+#global knitr settings to determine the output of the markdown document upon 'knitting'
+knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(root.dir = paste0(path))
+#Messages and warnings are turned off globally for a cleaner output. Change to TRUE for complete output
+knitr::opts_chunk$set(message = FALSE)
+knitr::opts_chunk$set(warning = FALSE)
+knitr::opts_chunk$set(tidy = TRUE)
+#CuPhyR is the author's own package that contains several functions used to process phyloseq objects. It is hosted on GitHub and installed/updated using this command if update_cuphyr is TRUE
+if (update_cuphyr | !"cuphyr" %in% rownames(installed.packages())) {
+devtools::install_github("simeross/cuphyr")
+}
+#Loading required packages
+library(phyloseq)
+library(dada2)