inst/rmarkdown/templates/analysis/skeleton/skeleton.md

In rasilab/rasilabRtemplates: Loads Templates For Rasi Lab Use

Template for analysis in R

rasi 15 April, 2018

Analysis Instructions

• This is an example outline of how we analyze data in our lab.
• When you have finished the current round of analysis, use the Knit to github_document button in the tool bar above to generate a regular .md file and any associated image files.
• Commit the .Rmd, .md and the _files folder to the lab Github repo.
• Use scale_color_manual(values = cbPalette) and scale_fill_manual(values = cbPalette) for all plots. cbPalette is exported by the rasilabRtemplates package.

Import libraries

# string manipulation functions
library(stringr)
# standard analysis and plotting functions, includes dplyr, ggplot2 
library(tidyverse)
# loads lab default ggplot2 theme and provides color-blind friendly palette
library(rasilabRtemplates)

Import data

data <- read_csv("https://github.com/tidyverse/readr/raw/master/inst/extdata/mtcars.csv") %>% 
  print()

## # A tibble: 32 x 11
##      mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
##    <dbl> <int> <dbl> <int> <dbl> <dbl> <dbl> <int> <int> <int> <int>
##  1  21.0     6  160.   110  3.90  2.62  16.5     0     1     4     4
##  2  21.0     6  160.   110  3.90  2.88  17.0     0     1     4     4
##  3  22.8     4  108.    93  3.85  2.32  18.6     1     1     4     1
##  4  21.4     6  258.   110  3.08  3.22  19.4     1     0     3     1
##  5  18.7     8  360.   175  3.15  3.44  17.0     0     0     3     2
##  6  18.1     6  225.   105  2.76  3.46  20.2     1     0     3     1
##  7  14.3     8  360.   245  3.21  3.57  15.8     0     0     3     4
##  8  24.4     4  147.    62  3.69  3.19  20.0     1     0     4     2
##  9  22.8     4  141.    95  3.92  3.15  22.9     1     0     4     2
## 10  19.2     6  168.   123  3.92  3.44  18.3     1     0     4     4
## # ... with 22 more rows

Transform data

processed_data <- data %>% 
  filter(am == 1) %>%
  select(mpg, qsec, carb)

processed_data %>% 
  knitr::kable()

| mpg | qsec | carb | | ---: | ----: | ---: | | 21.0 | 16.46 | 4 | | 21.0 | 17.02 | 4 | | 22.8 | 18.61 | 1 | | 32.4 | 19.47 | 1 | | 30.4 | 18.52 | 2 | | 33.9 | 19.90 | 1 | | 27.3 | 18.90 | 1 | | 26.0 | 16.70 | 2 | | 30.4 | 16.90 | 2 | | 15.8 | 14.50 | 4 | | 19.7 | 15.50 | 6 | | 15.0 | 14.60 | 8 | | 21.4 | 18.60 | 2 |

Plot data

processed_data %>% 
  gather(statistic, value, -carb) %>% 
  ggplot(aes(x = carb, y = value, color = statistic)) +
  facet_wrap(~ statistic, ncol = 2) +
  geom_jitter(width = 0) +
  scale_color_manual(values = cbPalette)

rasilab/rasilabRtemplates documentation built on March 28, 2023, 8:05 p.m.