R FOR CHEMISTS
GETTING STARTED
1
installation
1.1
R
1.2
RStudio
1.3
Verification
1.4
tidyverse
1.5
TeX
1.6
phylochemistry
1.7
xcms
1.8
Updating R and R Packages
DATA VISUALIZATION
2
ggplot and markdown
2.1
Objects
2.2
Functions
2.3
ggplot
2.3.1
modifying geoms
2.3.2
multiple geoms
2.4
markdown
2.5
exercises
2.5.1
Algae Chemistry Dataset
2.6
Alaska Lakes Dataset
3
geoms, facets, scales, themes
3.1
geoms
3.2
facets
3.3
scales
3.3.1
RColorBrewer
3.4
themes
3.4.1
Complete themes
3.4.2
Theme components
3.5
exercises
4
import and tidying
4.1
data import
4.2
tidy data
5
the pipe and summaries
5.1
the pipe (%>%)
5.2
summary statistics
5.3
exercises
CHEMOMETRICS
6
clustering
6.1
theory
6.2
exercises
7
pca
7.1
pca
7.2
ordination plots
7.3
principal components
7.4
exercises
7.4.1
option 1: human metabolomics.
7.4.2
option 2: grape vine chemistry
8
k-means
8.1
theory
8.2
exercises
8.2.1
Question 1
8.2.2
Question 2
8.2.3
Question 3
8.2.4
Question 4
8.2.5
Question 5
8.2.6
Question 6
8.2.7
Question 7
8.2.8
Challenge (optional)
9
models
9.1
theory
9.2
exercises
10
comparing means
10.1
definitions
10.2
test selection
10.3
two means
10.4
more than two means
10.4.1
ANOVA, Tukey tests
10.4.2
Kruskal, Dunn tests
10.5
pairs of means
10.6
further reading
10.7
exercises
WRITING
11
figures & captions
12
results and discussion
12.1
structure
12.2
suggestions
13
conclusion and introduction
13.1
structure
13.2
suggestions
14
abstract and title
14.1
abstract
14.2
title
14.3
further reading
IMAGE ANALYSIS
15
image color analysis
16
images of mass spectra
APPENDIX
17
links
17.1
geoms
17.2
colors
18
faq
18.1
filtering
18.2
ordering
18.3
column manipulation
19
templates
19.1
matrix analyses
19.1.1
basic
runMatrixAnalysis()
template
19.1.2
advanced
runMatrixAnalysis()
template
R For Chemists
16
images of mass spectra
analyzeMassSpectralImages
()