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10_faceting_plots.md

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Raw
layout title output
lesson
Session 10: Faceting your figures
markdown_document

Learning objectives

source("code/baxter.R")

alpha <- read_tsv(file="raw_data/baxter.groups.ave-std.summary",
		col_types=cols(group = col_character())) %>%
	filter(method=='ave') %>%
	select(group, sobs, shannon, invsimpson, coverage)
metadata <- get_metadata()
meta_alpha <- inner_join(metadata, alpha, by=c('sample'='group'))

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_grid(.~metric)

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_grid(metric~.)

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_grid(sex~metric)

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_wrap(~metric)

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_wrap(~metric, scales="free")

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_wrap(sex~metric, scales="free")

meta_alpha %>% pivot_longer(c(shannon, invsimpson, sobs, coverage), names_to="metric", values_to="value") %>% ggplot(aes(x=diagnosis, y=value)) + geom_boxplot() + facet_wrap(sex~metric, scales="free", nrow=2)

#customize labels for panels http://ggplot2.tidyverse.org/reference/labeller.html http://ggplot2.tidyverse.org/reference/as_labeller.html http://ggplot2.tidyverse.org/reference/labellers.html capitalize <- function(string) { substr(string, 1, 1) <- toupper(substr(string, 1, 1)) string } p2 <- ggplot(msleep, aes(x = sleep_total, y = awake)) + geom_point() p2 + facet_grid(vore ~ conservation, labeller = labeller(vore = capitalize))

conservation_status <- c( cd = "Conservation Dependent", en = "Endangered", lc = "Least concern", nt = "Near Threatened", vu = "Vulnerable", domesticated = "Domesticated" ) p2 + facet_grid(vore ~ conservation, labeller = labeller( .default = capitalize, conservation = conservation_status ))

#ordination with gray background points and colored top points ggplot(mpg, aes(displ, hwy)) + geom_point(data = transform(mpg, class = NULL), colour = "grey85") + geom_point() + facet_wrap(~class)

gganimate

cowplot