CRISPRi_library_2019.yml

# variables to generate gene tree
tree:
  levels:
    - Process.abbr
    - Pathway.abbr
    - Gene.names
    - Protein
  gene_level:
    - Gene.names

# main parameters to filter data
data:
  condition:
    values:
      - L100
      - L300
      - LAC
      - LD
      - NACL
    selected:
      - L100
  timepoint:
    values:
      - 0
      - 1
      - 2
      - 4
      - 8
      - 16
      - 32
    selected:
      - 0
      - 1
      - 2
      - 4
      - 8
      - 16
      - 32
  induction:
    values:
      - i
      - u
    selected:
      - i
      - u

# variables for plotting data
plotting:
  x_vars:
    - timepoint
    - generations
    - condition
    - induction
    - sgRNA_short
    - locus
    - Protein
    - Process
    - Pathway
  y_vars:
    - FoldChange
    - fitness_score
    - baseMean
    - padj
  cond_vars:
    - sgRNA_short
    - timepoint
    - generations
    - condition
    - induction
    - locus
    - Protein
    - Process
    - Pathway

# default plot parameters
default:
  theme:
    - lattice grey
    - lattice blue
    - ggplot1
    - ggplot2
  grouping:
    - by induction
    - by cond. variable
    - by X variable
    - by Y variable
    - by condition
    - none
  plot_type:
    - points and lines
    - points
    - lines
  y_scale:
    - log 2
    - log 10
    - log e
    - linear
  fitness:
    x_var: sgRNA
    y_var: fitness_score
    comparison: condition
    filter:
      var: timepoint
      val: 0