My most Google'd R code.

R tips and tricks

You know that pile of bookmarks hidden in a subdirectory? Or those pages Google reminds you that you 'visited many times'? Here, I collect all that code in one place. It's mostly for me but if you find it useful, go for it!

Table of Contents

Rmarkdown
ggplot
Tables
- Manipulation
- kableExtra
Symbols and math
Shiny
Other R posts

Rmarkdown

Default YAML header

---
title: 'TITLE'
subtitle: 'SUBTITLE'
author: "Kim Dill-McFarland, kadm@uw.edu"
date: "version `r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    toc: yes
    toc_depth: 4
    toc_float:
      collapsed: no
editor_options:
  chunk_output_type: console
always_allow_html: true
fig_width: 8.5
---

ggplot

Color

ColorBrewer

Emulate ggplot scales::hue_pal()(4)

Design seeds

Shape

Axes

Rotate theme(axis.text.x = element_text(angle = 45, hjust = 1))

Reorder ggplot(aes(x=reorder(x.var, y.var), y=y.var))

Log scale scale_y_log10()

Remove all labels

theme(axis.title.x=element_blank(),
      axis.text.x=element_blank(),
      axis.ticks.x=element_blank())

Relabel facets

facet_grid(~ varaible, labeller = as_labeller(c( "orig1" = "new1", "orig2 = "new2")))

Special characters

'italic("In vivo")~"TEXT"*alpha'
facet_wrap(~facet.lab, labeller = label_parsed)

Statistics

Add summary statistic stat_summary(fun="mean", geom="crossbar")

Add P-value stat_compare_means(method="wilcox.test")

Specific plot types

Draw polygons around points

Flowcharts

Networks

Label all points

geom_text_repel(aes(label = rowname), direction = "both",
                nudge_x = -0.4, min.segment.length = unit(0, 'lines'),
                show.legend = FALSE, max.overlaps = 100)

Barplot up to 100%

geom_bar(position = "fill", stat = "identity")

Side-by-side barplot

geom_bar(stat = "identity", position = 'dodge')

Connect jittered points

geom_line(aes(group = pair), position = position_dodge(0.2)) +
geom_point(aes(group = pair), position = position_dodge(0.2)) +

Tables

Manipulation

List to data frame

plyr::ldply(l, data.frame)

kableExtra

Standard table format

kable() %>%
kable_styling(bootstrap_options = "striped", full_width = FALSE)

Format column

column_spec(1, bold = TRUE, background = "yellow", border_right = TRUE)

add_header_above(c(" ", "Group 1" = 2, "Group 2" = 2, "Group 3" = 2))

Row format

row_spec(1, bold = TRUE, background = "yellow")

pack_rows("Group 1", 4, 7)

Format cell

dat$col <- cell_spec(dat$col, color = ifelse(dat$col <= 0.05, "red", "black"))

kable(escape = FALSE) %>%
kable_styling(bootstrap_options = "striped")

Symbols and math

Greek letters \alpha

Arrow \to

Sub/superscript k_sub^super

Fraction \frac{numerator}{denominator}

Plus/minus \pm

Shiny

Widgets