Chronobiome Data Analyses

Amy Campbell & Nicholas Lahens, 2016

Repo Contents

• chronobiome.sh
  • Shell script, runs the scripts below
  • User run shell script anywhere by specifing directory containing the R scripts below
• install.R
  • Installs necessary R dependencies
  • Saves record of installation with checkpoint package
  • Outputs:
    • session.info.txt
• Process_Activity_Communication_BP.R
  • Assigns common hour/subject index to all datapoints in activity, communication, blood pressure/HR, and energy data
  • Transforms activity and communication variables to improve normality
  • Outputs:
    • transformed.community.activity.csv
    • community.activity.csv
    • heartrate.bp.csv
    • energy.csv
• Variance_Correlation_Plot.R
  • Generates R-squared (variability explained) heatmaps for activity & communication variables for all 4 months and for activity, communication, and blood pressure / heart rate variables
  • Generates p-value (from linear model fitting) heatmaps for activity & communication variables for all 4 months and for activity, communication, and blood pressure / heart rate variables
  • Clusters subjects and generates dendrograms for p-values (from linear model fitting) across activity & communication variables for all 4 months and for activity, communication, and blood pressure / heart rate variables
  • Generates .pdf of scatterplots for each activity, communication, energy, and blood pressure/heartrate variable against each other
  • Outputs:
    • Variability.Act.Com.BP.eps
    • Varability.Act.Com.BP.Visit1.Feb.eps
    • Varability.Act.Com.BP.Visit2.Feb.eps
    • Variance_Explained_WithEnergy.eps
    • HCR001_Variance.4months.eps
    • HCR003_Variance.4months.eps
    • HCR004_Variance.4months.eps
    • HCR006_Variance.4months.eps
    • HCR008_Variance.4months.eps
    • HCR009_Variance.4months.eps
    • Variability.Activity.Communication.eps
    • HCR001_Variance.4months_withEnergy
    • HCR003_Variance.4months_withEnergy
    • HCR004_Variance.4months_withEnergy
    • HCR006_Variance.4months_withEnergy
    • HCR008_Variance.4months_withEnergy
    • HCR009_Variance.4months_withEnergy
    • Variability.Activity.Communication_WithEnergy.eps
    • HCR001_Variance_BothVisits
    • HCR003_Variance_BothVisits
    • HCR004_Variance_BothVisits
    • HCR006_Variance_BothVisits
    • HCR008_Variance_BothVisits
    • HCR009_Variance_BothVisits
    • HCR001_Variance_visit1
    • HCR003_Variance_visit1
    • HCR004_Variance_visit1
    • HCR006_Variance_visit1
    • HCR008_Variance_visit1
    • HCR009_Variance_visit1
    • HCR001_Variance_visit2
    • HCR003_Variance_visit2
    • HCR004_Variance_visit2
    • HCR006_Variance_visit2
    • HCR009_Variance_visit2
• PCAPlot.R
  • Performs PCA on combined activity and communication data across all 4 months
  • Repeat PCA excluding the circadian stats (signal, period, amplitude, phase) from the luminescence, mobility, and mobility radius metrics
  • Plots activity and communication PCA, and plots metabolomic and microbiomic PCAs performed by Seth Rhodes
  • Outputs:
    • Act_Com_PCAPlotAll.eps
    • Act_Com_PCAPlot_48.eps
    • Act_Com_PCAPlotAll.no_circ_stats.eps
    • Act_Com_PCAPlot_48.no_circ_stats.eps
    • Facets_Act_Com_PC2PC3.eps
    • Facets_Act_Com_PC1PC3.eps
    • Facets_Act_Com_PC2PC3.eps
    • Facets_Act_Com_PC2PC3.no_circ_stats.eps
    • Facets_Act_Com_PC1PC3.no_circ_stats.eps
    • Facets_Act_Com_PC2PC3.no_circ_stats.eps
    • Saliva_Metabs_PCA.eps
    • Saliva_Microbes_PCA.eps
    • Plasma_Proteins_PCA.eps
    • Plasma_Metabs_PCA.eps
    • Macronutrients.eps