DoveParentsRNAseq: Dove Parents RNAseq

# custom themes

## hex colors chosen using https://colorbrewer2.org/ 
## hex colors blended using from https://meyerweb.com/eric/tools/color-blend/#F8766D:D39200::hex 

theme_B3 <- function () { 
  theme_classic(base_size = 7,
                base_family = 'Helvetica') +
    theme(
      strip.background  = element_blank(),
      panel.grid.major  = element_blank(),  # remove major gridlines
      panel.grid.minor  = element_blank()  # remove minor gridlines
    )
}

# custom levels

# characterization
charlevels <- c("control", "bldg", "lay", "inc.d3", "inc.d9", "inc.d17", "hatch", "n5", "n9")
charlevelsnocontrol <- c( "bldg", "lay", "inc.d3", "inc.d9", "inc.d17", "hatch", "n5", "n9")
maniplevels <- c("m.inc.d3" ,  "early" ,  "m.inc.d9" , "m.inc.d17", "prolong" ,  "m.n2", "extend")

# manipulation
timinglevels <- c("inc.d3", "inc.d9", "inc.d17", "early" , "prolong" ,  "extend")

removallevels <- c( "m.inc.d3" ,  "m.inc.d9" ,
             "m.inc.d17" ,  "m.n2")

# mix of characterization and manipulation, ordered by time
alllevels <- c("control", "bldg", "lay", "inc.d3", "m.inc.d3" ,  
               "inc.d9", "m.inc.d9" , "early" ,
               "inc.d17",  "m.inc.d17", "prolong", 
               "hatch",  "m.n2", "extend",
               "n5",  
               "n9")

alllevelsnochar <- c("lay", "inc.d3", "m.inc.d3" ,  
                     "inc.d9", "m.inc.d9" , "early" ,
                     "inc.d17",  "m.inc.d17", "prolong", 
                     "hatch",  "m.n2", "extend",
                     "n5",  
                     "n9")

alllevelswithmanip <- c("inc.d3", "m.inc.d3" ,  
                        "inc.d9", "m.inc.d9" , "early" ,
                        "inc.d17",  "m.inc.d17", "prolong", 
                        "hatch",  "m.n2", "extend",
                        "n5")

# characteriation first, then manip by time
alllevels2 <- c("control", "bldg", "lay", "inc.d3", "inc.d9", 
                "inc.d17", "hatch", "n5", "n9",
                "m.inc.d3" ,   "m.inc.d9" , "m.inc.d17"  , "m.n2", 
                "early" , "prolong", "extend")

deseq2levels <- c("bldg", "control", "lay", "inc.d3", "inc.d9", 
                "inc.d17", "hatch", "n5", "n9",
                "m.inc.d3" ,   "m.inc.d9" , "m.inc.d17"  , "m.n2", 
                "early" , "prolong", "extend")

hypothesislevels <- c(  "nest",  "eggs", "chicks" ,  "lo" , "hi" , "early", "late")

# tissue
tissuelevels <- c("hypothalamus", "pituitary", "gonads")
tissuelevel <- c("hypothalamus", "pituitary", "gonad")
myshapes = c("hypothalamus" = 20,  "pituitary" = 17,  "gonads" = 15)

# sex
sexlevels <- c("female", "male")

# DESeq
levelssequential <- c("bldg_lay",  "lay_inc.d3",  
                          "inc.d3_inc.d9",   "inc.d9_inc.d17",  
                          "inc.d17_hatch", "hatch_n5", "n5_n9")

labelsssequential <- c("lay",  "inc.d3",  
                       "inc.d9",   "inc.d17",  
                       "hatch", "n5", "n9")

levelsmanip <- c("inc.d3_m.inc.d3", "inc.d9_m.inc.d9",  "early_inc.d9" ,
                           "hatch_early",  "inc.d17_m.inc.d17", 
                 "inc.d17_prolong",
                 "hatch_m.n2",  "hatch_prolong",
                          "extend_hatch", "n5_extend")

labelssmanip <- c("inc.d3_m.inc.d3", "inc.d9_m.inc.d9",  "early_inc.d9" ,
                  "hatch_early",  "inc.d17_m.inc.d17", 
                  "inc.d17_prolong",
                  "hatch_m.n2", "hatch_prolong",
                  "extend_hatch", "n5_extend")

levelsinc9 <- c("inc.d9_m.inc.d9", "inc.d9_early")
levelsinc17 <- c("inc.d17_m.inc.d17", "inc.d17_prolong")
levelshatch <- c("hatch_m.n2", "hatch_early", "hatch_prolong", "hatch_extend" )
levelsearly <- c("early_prolong", "early_extend")

levelsmanip <- c(levelsinc9,levelsinc17,  levelshatch )

levelsrm <- c("inc.d3_m.inc.d3", "inc.d9_m.inc.d9","inc.d17_m.inc.d17",  "hatch_m.n2" )
levelsreplace <- c("inc.d9_early","inc.d17_prolong", "hatch_early", "hatch_prolong", "hatch_extend")

labelsinc9 <- c("m.inc.d9", "early")
labelsinc17 <- c("m.inc.d17", "prolong")
labelshatch <- c("m.n2", "early",  "prolong", "extend")
labelsearly <- c("prolong", "extend")

levelscontrolcharmanip <- c("bldg_control", "control_lay",  "control_inc.d3",  
                             "control_inc.d9",   "control_inc.d17",  
                             "control_hatch", "control_n5", "control_n9",
                            
                             "control_m.inc.d3", "control_m.inc.d9",  
                             "control_m.inc.d17","control_m.n2",
                            "control_early", "control_prolong", "control_extend"
                            )

labelscontrolcharmanip  <- c("bldg" ,"lay", "inc3", 
                             "inc9", "inc17", 
                             "hatch" , "n5", "n9",
                             "m.inc3", "m.inc9",
                             "m.inc17", ".m.n2" ,
                             "early" , "prolong", "extend"
                             )


levelsbldgchar <- c("bldg_control", "bldg_lay",  "bldg_inc.d3",  
                            "bldg_inc.d9",   "bldg_inc.d17",  
                            "bldg_hatch", "bldg_n5", "bldg_n9"
                            )

labelsbldgchar  <- c("control", "lay", "inc3", 
                             "inc9", "inc17", 
                             "hatch" , "n5", "n9"
                             )


# contrastst part 1. versus control and bldg
#references <- c("control", "bldg")
references <- c("bldg")

# contrastst part 2. manips versus internal or other manips
manipcontrols <- c("inc.d9", "inc.d17", "hatch", "n5",  "prolong", "early")
replacements   <- c("early", "prolong", "extend")

# custom colors

colorschar <-  c("control" = "#cc4c02", 
                 "bldg"= "#fe9929", 
                 "lay"= "#fed98e", 
                 "inc.d3"= "#78c679", 
                 "inc.d9"= "#31a354", 
                 "inc.d17"= "#006837", 
                 "hatch"= "#6baed6",
                 "n5"= "#3182bd", 
                 "n9"= "#08519c" )

colorsmanip <- c("m.inc.d3" = "#CDCDCD", 
                 "m.inc.d9" = "#959595", 
                 "m.inc.d17" = "#626262",
                 "m.n2" = "#262625", 
                 "early" = "#cbc9e2", 
                 "prolong" = "#9e9ac8" , 
                 "extend" = "#6a51a3" )

colorscharmaip <-  c(colorschar, colorsmanip)

colorsnewgrouping <-  c("control" = "#F8766D", 
                 "bldg"= "#D39200", 
                 "earlyinc"= "#00C19F", 
                 "nearhatch"= "#619CFF", 
                 "chickcare"= "#FF61C3",
                 "manip" = "#959595")

colorhypothesis <- c("none" = "#cc5500",
                     "loss" = "#8B4513",
                     "eggs" = "#7FA163",
                     "chicks" = "#3A80B9",
                     "lo" = "#B5C4B2",
                     "hi" = "#19757A",
                     "early" = "#B5C4B2",
                     "late" = "#19757A",
                     "reference" = "#F8766D" ,
                     "earlier" = "#B5C4B2",
                     "later" = "#19757A",
                     "control" = "#F8766D",
                     "controls" = "#F8766D")

levelhypothesis <- c("reference", "eggs", "chicks", "loss", "early", "late")

colorstissue <- c("hypothalamus" = "#d95f02",
                  "pituitary" = "#1b9e77",
                  "gonads" =  "#7570b3",
                  "gonad" =  "#7570b3")

sexcolors <- c("female" = "#969696", "male" = "#525252",
               "f" = "#969696", "m" = "#525252")

colorsvolcano <-  c(colorschar,
                    
                    "early" = "#cbc9e2", 
                    "prolong" = "#9e9ac8" , 
                     "extend" = "#6a51a3",
                    
                    "male" = "#525252",
                    "female" = "#969696",
                    
                    "NS" = "#bdbdbd")

 
allcolors <- c(colorscharmaip, sexcolors, 
               colorstissue, colorhypothesis)
 
colorsvolcanochar <-  c(colorschar,
                    "NS" = "#bdbdbd")

myannotationcolors <- list(sex = sexcolors,
                        tissue = colorstissue,
                        treatment = colorscharmaip)