https://github.com/meglab2017/The-microbial-biosphere-of-the-coral-Acropora-cervicornis-in-Northeastern-Puerto-Rico
Revision acf5851080b5159b1e19b3afd81d9782f203f9b4 authored by meglab2017 on 15 August 2017, 02:21:33 UTC, committed by GitHub on 15 August 2017, 02:21:33 UTC
1 parent 6ecc1f9
Tip revision: acf5851080b5159b1e19b3afd81d9782f203f9b4 authored by meglab2017 on 15 August 2017, 02:21:33 UTC
Update README.md
Update README.md
Tip revision: acf5851
taxa_summary_genus_script.R
require(ggplot2)
require(reshape2)
dat <- read.table("/Users/AbbyARivera/Desktop/MEGL/Corales/Data_Jul_12_17/genus_figure_R/taxonomy_L6_R.txt", sep = "\t", header = T)
colors <- c("#660000",
"#990000",
"#FF0000",
"#FF6666",
"#FFCCCC",
"#663300",
"#994C00",
"#FF8000",
"#FFB266",
"#FFE5CC",
"#666600",
"#999900",
"#FFFF00",
"#FFFF66",
"#FFFFCC",
"#336600",
"#4C9900",
"#80FF00",
"#B2FF66",
"#E5FFCC",
"#006633",
"#00CC66",
"#33FF99",
"#99FFCC",
"#CCFFE5",
"#006666",
"#009999",
"#00FFFF",
"#99FFFF",
"#CCFFFF",
"#003366",
"#004C99",
"#0080FF",
"#66B2FF",
"#CCE5FF",
"#000099",
"#0000FF",
"#6666FF",
"#9999FF",
"#CCCCFF",
"#330066",
"#6600CC",
"#9933FF",
"#CC99FF",
"#E5CCFF",
"#660066",
"#990099",
"#FF00FF",
"#FF66FF",
"#FFCCFF",
"#660033",
"#99004C",
"#FF007F",
"#FF66B2",
"#FFCCE5",
"#000000",
"#404040",
"#808080",
"#C0C0C0",
"#FFFFFF",
"#AFEEEE")
dat$Facet <- factor(dat$Facet, c(""All Taxa", "Non-Ricketsialles Taxa""))
dat.m <- melt(dat, id = c("Taxonomy", "Facet"))
plot <- ggplot(dat.m, aes(variable, fill = Taxonomy, weight = value))
plot + geom_bar(position = "fill", width = 0.98) + scale_fill_manual(values = colors[1:length(dat$Taxonomy)] ) + facet_grid(. ~ Facet) +
scale_y_continuous(expand = c(0, 0.005)) + scale_x_discrete(expand = c(0.005, 0)) +
theme_bw() + theme(axis.text.x = element_text(size =15, angle = 0),
axis.title.x = element_text(size=15),
axis.text.y = element_text(size =15, angle = 0, hjust = 1, vjust = 0.35),
axis.title.y = element_text(size = 15),
strip.text = element_text(size = 15),
legend.title = element_text(size=15),
legend.text = element_text( size = 15)) +
xlab("Samples") + ylab("Proportion")
ggsave("/Users/AbbyARivera/Desktop/MEGL/Corales/Data_Jul_12_17/genus_figure_R/figure_L6.tiff", height = 10, width = 20, units = "in")
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