Record Keeping in Computing Good enough practices in scientific - PowerPoint PPT Presentation

Record Keeping in Computing Good enough practices in scientific computing Greg Wilson 1 ☯ * , Jennifer Bryan 2 ☯ , Karen Cranston 3 ☯ , Justin Kitzes 4 ☯ , Lex Nederbragt 5 ☯ , Tracy K. Teal 6 ☯ ☯ * ☯ ☯ ☯ ☯ ☯ http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510 ☯ ☯ OPEN ACCESS OPEN ACCESS © ©

Record Keeping in Computing

Record Keeping in Computing Introduction to R and R Markdown https://dbsloan.github.io/TS2019/exercises/r_markdown.html

Data Visualization Images: Circos.ca

Data Visualization

Data Visualization Quality Figures for Papers and Presentations • Clear and accurate representation of your data • Clean, professional, and aesthetically pleasing appearance • Efficient, reproducible, and automated

Data Visualization Writing Code to Generate Figures ggplot(cnld) + geom_point(aes(x=CumPos, y=r2, size=0.75, colour=as.factor(ChromPrint), alpha = 1/8)) + scale_size_identity() + theme_bw(base_size=15) + scale_color_manual(values=c(rep(c('black', 'dark gray'),11), 'black', 'red')) + scale_x_continuous(expand = c(0.015, 0.015),labels=c(as.character(1:chrNum), "X"), breaks=bpMidVec) + theme(plot.margin = unit( c(0.03,0.03,0.03,0.03) , "in" ), legend.position='none', axis.text.x = element_text(size=6), axis.text.y = element_text(size=7), axis.title.x = element_text(size=8), axis.title.y = element_text(size=8)) + xlab('Chromosome Position') + ylab(expression(paste("Mitonuclear LD (",r^2, ")")))

Data Visualization Gene Expression (RNA-seq Read Depth) Chromosome Position (kb)

Data Visualization Plotting Genomic Data with R and ggplot https://dbsloan.github.io/TS2019/exercises/ggplot.html

Data Visualization Portiera BT (244.9-278.6 kb) Portiera TV (183.5-203.6 kb)

Data Visualization

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Data Visualization Figure Drawing in R https://dbsloan.github.io/TS2019/exercises/r_figure_drawing.html

Data Visualization

Data Visualization Visualizing Genomic Data with Circos https://dbsloan.github.io/TS2019/exercises/circos.html