Cupriavidus_BarSeq_2023.yml

# variables to generate gene tree
tree:
  levels:
    - Process
    - Pathway
    - gene_name
    - locus_tag
  gene_level:
    - gene_name

# main parameters to filter data
data:
  condition:
    values:
      - hydrogen - pulse
      - nitrate - continuous
      - nitrate - pulse
      - fructose - continuous
      - fructose - pulse
      - formate - continuous
      - formate - pulse
      - succinate - continuous
      - succinate - pulse
    selected:
      - hydrogen - pulse
      - nitrate - pulse
      - formate - pulse
  timepoint:
    values:
      - 0
      - 4
      - 8
      - 12
      - 16
    selected:
      - 0
      - 4
      - 8
      - 12
      - 16

# variables for plotting data
plotting:
  x_vars:
    - timepoint
    - condition
    - locus_tag
    - gene_name
    - Process
    - Pathway
  y_vars:
    - fitness_score
    - fold_change
    - t_stat
    - counts
    - strains_per_gene
  cond_vars:
    - gene_name
    - locus_tag
    - timepoint
    - condition
    - Process
    - Pathway

# default plot parameters
default:
  theme:
    - lattice grey
    - lattice blue
    - ggplot1
    - ggplot2
  grouping:
    - by condition
    - by cond. variable
    - by X variable
    - by Y variable
    - none
  plot_type:
    - points and lines
    - points
    - lines
  y_scale:
    - linear
    - log 2
    - log 10
    - log e
  fitness:
    x_var: gene_name
    y_var: fitness_score
    comparison: condition
    filter:
      var: timepoint
      val: 8