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Record Keeping in Computing
Good enough practices in scientific computing
Greg Wilson1☯*, Jennifer Bryan2☯, Karen Cranston3☯, Justin Kitzes4☯, Lex Nederbragt5☯, Tracy K. Teal6☯
☯ OPEN ACCESS ©
☯* ☯ ☯ ☯ ☯ ☯
☯ OPEN ACCESS ©
Record Keeping in Computing Good enough practices in scientific - - PowerPoint PPT Presentation
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 *
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Record Keeping in Computing
https://dbsloan.github.io/TS2019/exercises/r_markdown.html
Introduction to R and R Markdown
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Data Visualization
Images: Circos.ca
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Data Visualization
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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
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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, ")")))
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Data Visualization
Gene Expression (RNA-seq Read Depth) Chromosome Position (kb)
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Data Visualization
https://dbsloan.github.io/TS2019/exercises/ggplot.html
Plotting Genomic Data with R and ggplot
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Data Visualization
Portiera BT (244.9-278.6 kb) Portiera TV (183.5-203.6 kb)
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Data Visualization
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Data Visualization
Diphylleia Thecamonas Homo Crassostrea Trichoplax Oscarella Mnemiopsis Allomyces Saccharomyces Monosiga Nuclearia Hartmannella Acanthamoeba Dictyostelium
- Ma. jakobiformis
- Ma. californiana
Reclinomonas Andalucia Naegleria Acrasis Amoeboid BB2 Tsukubamonas Trypanosoma Euglena gracilis Alexandrium Chromera Plasmodium Tetrahymena Colponemid−like Nyctotherus Chattonella Phaeodactylum Cafeteria Blastocystis Bigelowiella Paracercomonas Brevimastigomonas Emiliania Chrysochromulina Ancoracysta Rhodomonas Hemiselmis Palpitomonas Picozoan sp. MS584−11 Cyanidioschyzon Porphyra Glaucocystis Cyanophora Chlamydomonas Prototheca Pycnococcus Nephroselmis Mesostigma Marchantia Nicotiana rps16 rpl23 rpl35 rpl36 tatA tufA rpoC rpoB rpl34 rpl32 rpoD rpoA rpl27 rpl10 rpl1 atp3 ccmA rpl18 rpl19 secY co rpl31 rpl20 rps1 ccmC sdh4 rps10 nad10 sdh2 ccmB sdh3 rpl11 rps7 nad11 rps19 atp1 rps11 rpl2 nad8 ccmF rpl5 rpl14 rps2 atp4 rps8 rpl6 tatC rps4 rps14 nad9 rps13 nad7 rpl16 nad4L rps3 nad6 rps12 atp8 nad3 nad5 atp9 nad2 nad4 nad1 co co atp6 co cob Translation Transcription Complex I Complex II Complex III Complex IV Complex V Cyt C Maturation Membrane Transport Viridiplantae Gla Rho Crypt Hap Rhiz Stramen Alveolata Excavata Am Opisthokonta
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Data Visualization
https://dbsloan.github.io/TS2019/exercises/r_figure_drawing.html
Figure Drawing in R
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Data Visualization
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