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"set_theme_defaults.pdf"), - width = 8, # important to explicitly set these arguments - height = 4 # for reproducibility of graphs - # (otherwise will depend on size of Rstudio plots pane) -) - -# Add x and y axes at 0, decrease plot margins, -# remove extra space below 0, -# add some cushion to the right of the y-axis title and above x-axis title. -mtcars %>% ggplot() + - geom_point(aes(y = hp, x = wt)) + - labs(y = "Horsepower", x = "Weight") + - geom_hline(yintercept = 0) + - geom_vline(xintercept = 0) + - scale_y_continuous(expand = expansion(mult = c(0, 0.01))) + # get rid of space below 0 - scale_x_continuous(expand = expansion(mult = c(0, 0.01))) + # and at top/right of plot - # note that expand = c(0, 0) would remove any space beyond scale but - # that would lead the points with highest x or y values to get partially cut off - # so expand = expansion(mult = c(0, 0.01)) expands top/right by 1% - # see https://ggplot2.tidyverse.org/reference/expansion.html - set_theme( - y_title_margin = "r = 5", - x_title_margin = "t = 5", - plot_margin = unit(c(t = 2, r = 2, b = 2, l = 2), "pt") - ) -ggsave( - here("results", "figures", "set_theme_with_axes.pdf"), - width = 8, # important to explicitly set these arguments - height = 4 # for reproducibility of graphs - # (otherwise will depend on size of Rstudio plots pane) -) - -# Add colors and legend -mtcars %>% ggplot() + - geom_point(aes(y = hp, x = wt, - color = as.factor(cyl)), size = 2 # bigger size to see colors - ) + - labs(y = "Horsepower", x = "Weight", color = "Cylinders") + - geom_hline(yintercept = 0) + - geom_vline(xintercept = 0) + - scale_y_continuous(expand = expansion(mult = c(0, 0.01))) + # get rid of space below 0 - scale_x_continuous(expand = expansion(mult = c(0, 0.01))) + # and at top/right of plot - # note that expand = c(0, 0) would remove any space beyond scale but - # that would lead the points with highest x or y values to get partially cut off - # so expand = expansion(mult = c(0, 0.01)) expands top/right by 1% - # see https://ggplot2.tidyverse.org/reference/expansion.html - scale_color_colorblind() + - set_theme( - y_title_margin = "r = 5", - x_title_margin = "t = 5", - plot_margin = unit(c(t = 2, r = 2, b = 2, l = 2), "pt"), - legend_position = "right" # default in set_theme() is "none" - ) -ggsave( - here("results", "figures", "set_theme_with_colors.pdf"), - width = 8, # important to explicitly set these arguments - height = 4 # for reproducibility of graphs - # (otherwise will depend on size of Rstudio plots pane) -) - -# Histogram -mtcars %>% ggplot() + - geom_histogram(aes(x = wt)) + - labs(y = "Count", x = "Weight") + - scale_y_continuous(expand = expansion(mult = c(0, 0.01))) + - geom_hline(yintercept = 0) + # add horizontal axis; - # no vertical axis since histogram doesn't start at 0 - set_theme() -ggsave( - here("results", "figures", "set_theme_histogram.pdf"), - width = 8, # important to explicitly set these arguments - height = 4 # for reproducibility of graphs - # (otherwise will depend on size of Rstudio plots pane) -) +# Simple examples of using set_theme() to standardize graph formatting +# Sean Higgins + +# Note: I recommend saving figures as .eps, but here I save as .pdf so that +# the figures are easier to view on GitHub. + +# PACKAGES -------------------------------------------------------------------- +library(tidyverse) +library(ggthemes) # for colorblind palette +library(here) + +# FUNCTIONS ------------------------------------------------------------------- +# Read in set_theme function +source(here("scripts", "programs", "set_theme.R")) + +# DATA ------------------------------------------------------------------------ +# We will use the mtcars dataframe which was already loaded with tidyverse + +# ANALYSIS -------------------------------------------------------------------- +# Use the defaults +mtcars %>% ggplot() + + geom_point(aes(y = hp, x = wt)) + + labs(y = "Horsepower", x = "Weight") + + set_theme() +ggsave( + here("results", "figures", "set_theme_defaults.pdf"), + width = 8, # important to explicitly set these arguments + height = 4 # for reproducibility of graphs + # (otherwise will depend on size of Rstudio plots pane) +) + +# Add x and y axes at 0, decrease plot margins, +# remove extra space below 0, +# add some cushion to the right of the y-axis title and above x-axis title. +mtcars %>% ggplot() + + geom_point(aes(y = hp, x = wt)) + + labs(y = "Horsepower", x = "Weight") + + geom_hline(yintercept = 0) + + geom_vline(xintercept = 0) + + scale_y_continuous(expand = c(0, 0.01)) + # get rid of space below 0 + scale_x_continuous(expand = c(0, 0.01)) + # and at top/right of plot + # note that expand = c(0, 0) would remove any space beyond scale but + # that would lead the points with highest x or y values to get partially cut off + # so expand = c(0, 0.01) expands top/right by 1% + # see https://ggplot2.tidyverse.org/reference/expansion.html + set_theme( + y_title_margin = "r = 5", + x_title_margin = "t = 5", + plot_margin = unit(c(t = 2, r = 2, b = 2, l = 2), "pt") + ) +ggsave( + here("results", "figures", "set_theme_with_axes.pdf"), + width = 8, # important to explicitly set these arguments + height = 4 # for reproducibility of graphs + # (otherwise will depend on size of Rstudio plots pane) +) + +# Add colors and legend +mtcars %>% ggplot() + + geom_point(aes(y = hp, x = wt, + color = as.factor(cyl)), size = 2 # bigger size to see colors + ) + + labs(y = "Horsepower", x = "Weight", color = "Cylinders") + + geom_hline(yintercept = 0) + + geom_vline(xintercept = 0) + + scale_y_continuous(expand = c(0, 0.01)) + # get rid of space below 0 + scale_x_continuous(expand = c(0, 0.01)) + # and at top/right of plot + # note that expand = c(0, 0) would remove any space beyond scale but + # that would lead the points with highest x or y values to get partially cut off + # so expand = c(0, 0.01) expands top/right by 1% + # see https://ggplot2.tidyverse.org/reference/expansion.html + scale_color_colorblind() + + set_theme( + y_title_margin = "r = 5", + x_title_margin = "t = 5", + plot_margin = unit(c(t = 2, r = 2, b = 2, l = 2), "pt"), + legend_position = "right" # default in set_theme() is "none" + ) +ggsave( + here("results", "figures", "set_theme_with_colors.pdf"), + width = 8, # important to explicitly set these arguments + height = 4 # for reproducibility of graphs + # (otherwise will depend on size of Rstudio plots pane) +) + +# Histogram +mtcars %>% ggplot() + + geom_histogram(aes(x = wt)) + + labs(y = "Count", x = "Weight") + + scale_y_continuous(expand = c(0, 0.01)) + + geom_hline(yintercept = 0) + # add horizontal axis; + # no vertical axis since histogram doesn't start at 0 + set_theme() +ggsave( + here("results", "figures", "set_theme_histogram.pdf"), + width = 8, # important to explicitly set these arguments + height = 4 # for reproducibility of graphs + # (otherwise will depend on size of Rstudio plots pane) +)