CRISPRi_library_2022.yml

# variables to generate gene tree
tree:
  levels:
    - process
    - pathway
    - gene_name
    - protein
  gene_level:
    - gene_name

# main parameters to filter data
data:
  condition:
    values:
      - "HC, HL"
      - "HC, IL"
      - "HC, LL"
      - "HC, LL, -N"
      - "HC, LL, +FL"
      - "HC, LL, +G"
      - "LC, IL"
      - "LC, LL"
      - "LC, LL, +D, +G"
      - "LC, LL, +FL"
      - "LC, LL, +G"
    selected:
      - "HC, HL"
      - "LC, LL"
  time:
    values:
      - 0
      - 4
      - 8
      - 10
    selected:
      - 0
      - 4
      - 8
      - 10

# variables for plotting data
plotting:
  x_vars:
    - time
    - condition
    - sgRNA_target
    - gene_name
    - locus
    - protein
    - process
    - pathway
  y_vars:
    - FoldChange
    - fitness
    - baseMean
    - padj
  cond_vars:
    - sgRNA_target
    - time
    - condition
    - locus
    - protein
    - 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:
    - log 2
    - log 10
    - log e
    - linear
  fitness:
    x_var: sgRNA
    y_var: fitness
    comparison: condition
    filter:
      var: time
      val: 0