🎒
NGS for natural scientist
  • 1. Preface
    • How to use this book
    • Motivation
    • Genomic data science as a tool to biologist
    • Next Generation Science (also NGS)
  • 2. Getting started
    • A step by step pipeline tutorial
    • Sequencing chemistry explained by Illumina
    • Joining a course
    • RNA quality and Library prep
    • (optional) My click moment about "Why Linux"
  • 3. Good-to-know beforehand
    • Experiment design
    • Single-end and Paired-end
    • Read per sample and data size
    • Normalization - RPKM/FPKM/TPM
    • Gene annotation
  • 4. Setting up terminal
    • My Linux terminal
    • Linux environment
    • R and RStudio
    • PATH
  • 5. FASTQ and quality control
    • Getting FASTQ files from online database
    • FASTQ quality assessment
  • 6. Mapping/alignment and quantification
    • Salmon
    • DESeq2
  • 7. Visualization
  • 8. Single cell RNA-Seq
  • 9. AWS cloud and Machine Learning
    • Machine Learning in a nutshell
    • R vs Python
    • Setting up ML terminal
    • Data exploration
  • (pending material)
    • graphPad
    • readings for ML
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  1. (pending material)

graphPad

Previous(pending material)Nextreadings for ML

Last updated 3 years ago

library(ggplot2) #Basic barplot p<-ggplot(data=df, aes(x=dose, y=len)) + geom_bar(stat="identity")

#Horizontal bar plot p + coord_flip()

pbasic <- ggplot(data=basic, aes(x=group, y=mean_sc)) + geom_bar(stat="identity", width=0.5, color="blue", fill="white") + theme_minimal()

+ scale_x_discrete(limits=c("colA", "colC"))

+ geom_text(aes(label=len), vjust=-0.3, size=3.5) outside bar

+ geom_text(aes(label=len), vjust=1.6, color="white", size=3.5) inside bar

ANOVA

dat <- data.frame(Group = c("S1", "S1", "S2", "S2"), Sub = c("A", "B", "A", "B"), Value = c(3,5,7,8))

ggplot(dat, aes(Group, Value)) + geom_bar(aes(fill = Sub), stat="identity", position="dodge", width=.5) + geom_signif(stat="identity", data=data.frame(x=c(0.875, 1.875), xend=c(1.125, 2.125), y=c(5.8, 8.5), annotation=c("", "NS")), aes(x=x,xend=xend, y=y, yend=y, annotation=annotation)) + geom_signif(comparisons=list(c("S1", "S2")), annotations="*", y_position = 9.3, tip_length = 0, vjust=0.4) + scale_fill_manual(values = c("grey80", "grey20"))

http://www.sthda.com/english/wiki/ggplot2-barplots-quick-start-guide-r-software-and-data-visualization
http://www.sthda.com/english/wiki/one-way-anova-test-in-r
http://www.sthda.com/english/wiki/one-way-anova-test-in-r
https://cran.r-project.org/web/packages/ggsignif/vignettes/intro.html