Nothing
R/addAttributesDfChrSize.R
In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices
Defines functions
addAttributesDfChrSizeSimple
addNeworderColumn
addChrSizeColumn
addAttributesDfChrSize
Documented in
addAttributesDfChrSize
#' addAttributesDfChrSize
#' @description returns all cols. as character
#' @keywords internal
#' @return list of data.frames
#' @import crayon
addAttributesDfChrSize <- function(listOfdfChromSize,threshold,specialOTUNames
,centromereSize,MbThreshold,cenFactor
,chrWidth,specialChrWidth,squareness
,modifyChr=TRUE
,mymessage=TRUE) {
for (i in 1:length(listOfdfChromSize)) {
#
# remove columns without info. per karyotype
#
listOfdfChromSize[[i]][listOfdfChromSize[[i]]==""]<-NA
listOfdfChromSize[[i]]<- listOfdfChromSize[[i]][, !apply(is.na(listOfdfChromSize[[i]]), 2, all)]
# Does the data.frame have short and long info?
if(mymessage){
message("\nChecking columns from dfChrSize\n")
}
#################################################################################################
#
# let see if it is monocen
#
if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ) {
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste("\nOTU ",names(listOfdfChromSize)[[i]],"has all columns with info to have monocen. If not, you have to clean your data"))
)# message
}
attr(listOfdfChromSize[[i]], 'cenType') <- "monocen"
attr(listOfdfChromSize[[i]], 'indexStatus') <- "missing"
#
# if larger than 100 000 reduce
#
myn <- max(pmax(listOfdfChromSize[[i]]$longArmSize + listOfdfChromSize[[i]]$shortArmSize) )
exp <- floor(log(myn , base = 10 ) )
divisor2 <- 10^exp
threshold2 <- threshold/10
divisor2 <- ifelse((myn/divisor2) < threshold2, divisor2 <- 10^(exp-1), divisor2 )
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
listOfdfChromSize[[i]]$longArmSize <- listOfdfChromSize[[i]]$longArmSize/divisor2
listOfdfChromSize[[i]]$shortArmSize <- listOfdfChromSize[[i]]$shortArmSize/divisor2
if(divisor2 >= MbThreshold){
attr(listOfdfChromSize[[i]],"units") <- "Mb"
attr(listOfdfChromSize[[i]],"ytitle") <- "Mb"
} else {
attr(listOfdfChromSize[[i]],"units") <- "notMb"
attr(listOfdfChromSize[[i]],"ytitle") <- "notMb"
}
if(attr(listOfdfChromSize[i],"name") %in% specialOTUNames){
attr(listOfdfChromSize[[i]],"ytitle") <- "cM"
}
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
# if(cenFormat=="inProtein"){
# centromereSize2 <- 0
# }
if(attr(listOfdfChromSize[[i]],"ytitle")=="cM"){
chrWidth2 <-specialChrWidth
} else {
chrWidth2 <- chrWidth
}
r2 <- chrWidth2/(squareness*2)
attr(listOfdfChromSize[[i]],"r2") <- r2
attr(listOfdfChromSize[[i]],"centromere") <- (centromereSize2/divisor2)*cenFactor
listOfdfChromSize[[i]]$centromereSize <- (centromereSize2/divisor2)*cenFactor
#
# correcting for ruler collapseCen
#
if(modifyChr){
if(centromereSize2>0) {
listOfdfChromSize[[i]]$shortArmSize<-listOfdfChromSize[[i]]$shortArmSize-((centromereSize2/divisor2)*cenFactor)/2
listOfdfChromSize[[i]]$longArmSize <-listOfdfChromSize[[i]]$longArmSize -((centromereSize2/divisor2)*cenFactor)/2
}
listOfdfChromSize[[i]]$shortArmSize<-ifelse(listOfdfChromSize[[i]]$shortArmSize<0,0,listOfdfChromSize[[i]]$shortArmSize)
listOfdfChromSize[[i]]$longArmSize <-ifelse(listOfdfChromSize[[i]]$longArmSize <0,0,listOfdfChromSize[[i]]$longArmSize )
}
} else if(length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ) {
# end monocen success
##############################################################################################3
# let see if it is holocen
#
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," has all columns with info to have holocen. If not, you have to clean your data")))
) # message
}
attr(listOfdfChromSize[[i]], 'cenType') <- "holocen"
attr(listOfdfChromSize[[i]], 'indexStatus') <- "missing"
#
# if larger than 100 000 reduce
#
myn<-max(listOfdfChromSize[[i]]$chrSize)
exp<-floor(log(myn , base = 10 ) )
divisor2 <- 10^exp
threshold2 <- threshold/10
ifelse( (myn/divisor2)<threshold2, divisor2<-10^(exp-1) ,divisor2)
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
listOfdfChromSize[[i]]$chrSize <- listOfdfChromSize[[i]]$chrSize/divisor2
if(divisor2 >= MbThreshold){
attr(listOfdfChromSize[[i]],"units") <- "Mb"
attr(listOfdfChromSize[[i]],"ytitle") <- "Mb"
} else {
attr(listOfdfChromSize[[i]],"units") <- "notMb"
attr(listOfdfChromSize[[i]],"ytitle") <- "notMb"
}
if(attr(listOfdfChromSize[i],"name") %in% specialOTUNames){
attr(listOfdfChromSize[[i]],"ytitle") <- "cM"
# attr(listOfdfChromSize[[i]],"units") <- "cM"
}
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
# if(cenFormat=="inProtein"){
# centromereSize2 <- 0
# }
if(attr(listOfdfChromSize[[i]],"ytitle")=="cM"){
chrWidth2 <-specialChrWidth
} else {
chrWidth2 <- chrWidth
}
r2 <- chrWidth2/(squareness*2)
attr(listOfdfChromSize[[i]],"r2") <- r2
attr(listOfdfChromSize[[i]],"centromere") <- (centromereSize2/divisor2)*cenFactor
listOfdfChromSize[[i]]$centromereSize <- (centromereSize2/divisor2)*cenFactor
} # if holocen success
#
# let see if it is not monocen
#
else if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," does not have all columns with info to make a monocen.: ",
paste0(c(setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)) # pas
) # crayon
) # message
}
listOfdfChromSize[[i]]<-NA
} # fi
#
# let see if it is not holocen
#
else if (length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU",names(listOfdfChromSize)[[i]],"does not have all columns with info to make a holocen:",
paste0(c(setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)))
) #mess
}
listOfdfChromSize[[i]]<-NA
}
} # end for for (i in 1:length(listOfdfChromSize)) {
listOfdfChromSize<-listOfdfChromSize[!is.na(listOfdfChromSize)]
#
# rebuild with centromereSize
#
listOfdfChromSize <- lapply(listOfdfChromSize, function(x) makeCharCols(x) )
return(listOfdfChromSize)
}
##############
addChrSizeColumn<-function(listOfdfChromSize){
for ( i in 1:length(listOfdfChromSize)) {
if(inherits(listOfdfChromSize[[i]], "data.frame")) {
if(attr(listOfdfChromSize[[i]], "cenType")=="monocen"){
listOfdfChromSize[[i]]<-makeNumCols(listOfdfChromSize[[i]])
listOfdfChromSize[[i]]$chrSize<-listOfdfChromSize[[i]]$shortArmSize+listOfdfChromSize[[i]]$longArmSize
} # if
} # if
} # for
return(listOfdfChromSize)
}
################### ordering function
addNeworderColumn<-function(listOfdfChromSize,orderlist){
for (s in 1:length(listOfdfChromSize)){
if(inherits(listOfdfChromSize[[s]], "data.frame")) {
listOfdfChromSize[[s]]<-listOfdfChromSize[[s]][orderlist[[s]], ] # important THIS orders
listOfdfChromSize[[s]]$neworder<-1:nrow(listOfdfChromSize[[s]])
}
} # end for
return(listOfdfChromSize)
}
###################
addAttributesDfChrSizeSimple <- function(listOfdfChromSize,centromereSize=NA,threshold=35, mymessage=TRUE){
for (i in 1:length(listOfdfChromSize)) {
#
# remove columns without info. per karyotype
#
listOfdfChromSize[[i]][listOfdfChromSize[[i]]==""]<-NA
listOfdfChromSize[[i]]<- listOfdfChromSize[[i]][, !apply(is.na(listOfdfChromSize[[i]]), 2, all)]
# Does the data.frame have short and long info?
if(mymessage){
message("\nChecking columns from dfChrSize\n" ) # mess
}
#################################################################################################
#
# let see if it is monocen
#
if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ) {
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste("\nOTU ",names(listOfdfChromSize)[[i]],"has all columns with info to have monocen. If not, you have to clean your data"))
)# message
}
attr(listOfdfChromSize[[i]],'cenType') <- "monocen"
#
# if larger than 100 000 reduce
#
myn<-max(pmax(listOfdfChromSize[[i]]$longArmSize+listOfdfChromSize[[i]]$shortArmSize) )
exp<-floor(log(myn , base = 10 ) )
divisor2<-10^exp
threshold2<- threshold/10
divisor2<-ifelse((myn/divisor2)<threshold2,divisor2<-10^(exp-1),divisor2)
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
# listOfdfChromSize[[i]]$longArmSize <- listOfdfChromSize[[i]]$longArmSize /divisor2
# listOfdfChromSize[[i]]$shortArmSize<- listOfdfChromSize[[i]]$shortArmSize/divisor2
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
attr(listOfdfChromSize[[i]],"centromere") <- centromereSize2 #/divisor2
listOfdfChromSize[[i]]$centromereSize <- centromereSize2 #/divisor2
} # if monocen success
##############################################################################################3
# let see if it is holocen
#
else if(length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," has all columns with info to have holocen. If not, you have to clean your data")))
) # message
}
attr(listOfdfChromSize[[i]], 'cenType') <- "holocen"
#
# if larger than 100 000 reduce
#
myn<-max(listOfdfChromSize[[i]]$chrSize)
exp<-floor(log(myn , base = 10 ) )
divisor2 <- 10^exp
threshold2 <- threshold/10
ifelse( (myn/divisor2)<threshold2, divisor2<-10^(exp-1) ,divisor2)
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
# listOfdfChromSize[[i]]$chrSize <- listOfdfChromSize[[i]]$chrSize/divisor2
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
attr(listOfdfChromSize[[i]],"centromere") <- centromereSize2#/divisor2
listOfdfChromSize[[i]]$centromereSize <- centromereSize2#/divisor2
} # if holocen success
#
# let see if it is not monocen
#
else if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," does not have all columns with info to make a monocen.: ",
paste0(c(setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)) # pas
) # crayon
) # message
}
listOfdfChromSize[[i]]<-NA
} # fi
#
# let see if it is not holocen
#
else if (length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU",names(listOfdfChromSize)[[i]],"does not have all columns with info to make a holocen:",
paste0(c(setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)))
) #mess
}
listOfdfChromSize[[i]]<-NA
}
} # end for for (i in 1:length(listOfdfChromSize)) {
listOfdfChromSize<-listOfdfChromSize[!is.na(listOfdfChromSize)]
#
# rebuild with centromereSize
#
listOfdfChromSize <- lapply(listOfdfChromSize, function(x) makeCharCols(x) )
return(listOfdfChromSize)
}
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Defines functions addAttributesDfChrSizeSimple addNeworderColumn addChrSizeColumn addAttributesDfChrSize
Documented in addAttributesDfChrSize
#' addAttributesDfChrSize
#' @description returns all cols. as character
#' @keywords internal
#' @return list of data.frames
#' @import crayon
addAttributesDfChrSize <- function(listOfdfChromSize,threshold,specialOTUNames
,centromereSize,MbThreshold,cenFactor
,chrWidth,specialChrWidth,squareness
,modifyChr=TRUE
,mymessage=TRUE) {
for (i in 1:length(listOfdfChromSize)) {
#
# remove columns without info. per karyotype
#
listOfdfChromSize[[i]][listOfdfChromSize[[i]]==""]<-NA
listOfdfChromSize[[i]]<- listOfdfChromSize[[i]][, !apply(is.na(listOfdfChromSize[[i]]), 2, all)]
# Does the data.frame have short and long info?
if(mymessage){
message("\nChecking columns from dfChrSize\n")
}
#################################################################################################
#
# let see if it is monocen
#
if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ) {
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste("\nOTU ",names(listOfdfChromSize)[[i]],"has all columns with info to have monocen. If not, you have to clean your data"))
)# message
}
attr(listOfdfChromSize[[i]], 'cenType') <- "monocen"
attr(listOfdfChromSize[[i]], 'indexStatus') <- "missing"
#
# if larger than 100 000 reduce
#
myn <- max(pmax(listOfdfChromSize[[i]]$longArmSize + listOfdfChromSize[[i]]$shortArmSize) )
exp <- floor(log(myn , base = 10 ) )
divisor2 <- 10^exp
threshold2 <- threshold/10
divisor2 <- ifelse((myn/divisor2) < threshold2, divisor2 <- 10^(exp-1), divisor2 )
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
listOfdfChromSize[[i]]$longArmSize <- listOfdfChromSize[[i]]$longArmSize/divisor2
listOfdfChromSize[[i]]$shortArmSize <- listOfdfChromSize[[i]]$shortArmSize/divisor2
if(divisor2 >= MbThreshold){
attr(listOfdfChromSize[[i]],"units") <- "Mb"
attr(listOfdfChromSize[[i]],"ytitle") <- "Mb"
} else {
attr(listOfdfChromSize[[i]],"units") <- "notMb"
attr(listOfdfChromSize[[i]],"ytitle") <- "notMb"
}
if(attr(listOfdfChromSize[i],"name") %in% specialOTUNames){
attr(listOfdfChromSize[[i]],"ytitle") <- "cM"
}
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
# if(cenFormat=="inProtein"){
# centromereSize2 <- 0
# }
if(attr(listOfdfChromSize[[i]],"ytitle")=="cM"){
chrWidth2 <-specialChrWidth
} else {
chrWidth2 <- chrWidth
}
r2 <- chrWidth2/(squareness*2)
attr(listOfdfChromSize[[i]],"r2") <- r2
attr(listOfdfChromSize[[i]],"centromere") <- (centromereSize2/divisor2)*cenFactor
listOfdfChromSize[[i]]$centromereSize <- (centromereSize2/divisor2)*cenFactor
#
# correcting for ruler collapseCen
#
if(modifyChr){
if(centromereSize2>0) {
listOfdfChromSize[[i]]$shortArmSize<-listOfdfChromSize[[i]]$shortArmSize-((centromereSize2/divisor2)*cenFactor)/2
listOfdfChromSize[[i]]$longArmSize <-listOfdfChromSize[[i]]$longArmSize -((centromereSize2/divisor2)*cenFactor)/2
}
listOfdfChromSize[[i]]$shortArmSize<-ifelse(listOfdfChromSize[[i]]$shortArmSize<0,0,listOfdfChromSize[[i]]$shortArmSize)
listOfdfChromSize[[i]]$longArmSize <-ifelse(listOfdfChromSize[[i]]$longArmSize <0,0,listOfdfChromSize[[i]]$longArmSize )
}
} else if(length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ) {
# end monocen success
##############################################################################################3
# let see if it is holocen
#
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," has all columns with info to have holocen. If not, you have to clean your data")))
) # message
}
attr(listOfdfChromSize[[i]], 'cenType') <- "holocen"
attr(listOfdfChromSize[[i]], 'indexStatus') <- "missing"
#
# if larger than 100 000 reduce
#
myn<-max(listOfdfChromSize[[i]]$chrSize)
exp<-floor(log(myn , base = 10 ) )
divisor2 <- 10^exp
threshold2 <- threshold/10
ifelse( (myn/divisor2)<threshold2, divisor2<-10^(exp-1) ,divisor2)
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
listOfdfChromSize[[i]]$chrSize <- listOfdfChromSize[[i]]$chrSize/divisor2
if(divisor2 >= MbThreshold){
attr(listOfdfChromSize[[i]],"units") <- "Mb"
attr(listOfdfChromSize[[i]],"ytitle") <- "Mb"
} else {
attr(listOfdfChromSize[[i]],"units") <- "notMb"
attr(listOfdfChromSize[[i]],"ytitle") <- "notMb"
}
if(attr(listOfdfChromSize[i],"name") %in% specialOTUNames){
attr(listOfdfChromSize[[i]],"ytitle") <- "cM"
# attr(listOfdfChromSize[[i]],"units") <- "cM"
}
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
# if(cenFormat=="inProtein"){
# centromereSize2 <- 0
# }
if(attr(listOfdfChromSize[[i]],"ytitle")=="cM"){
chrWidth2 <-specialChrWidth
} else {
chrWidth2 <- chrWidth
}
r2 <- chrWidth2/(squareness*2)
attr(listOfdfChromSize[[i]],"r2") <- r2
attr(listOfdfChromSize[[i]],"centromere") <- (centromereSize2/divisor2)*cenFactor
listOfdfChromSize[[i]]$centromereSize <- (centromereSize2/divisor2)*cenFactor
} # if holocen success
#
# let see if it is not monocen
#
else if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," does not have all columns with info to make a monocen.: ",
paste0(c(setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)) # pas
) # crayon
) # message
}
listOfdfChromSize[[i]]<-NA
} # fi
#
# let see if it is not holocen
#
else if (length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU",names(listOfdfChromSize)[[i]],"does not have all columns with info to make a holocen:",
paste0(c(setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)))
) #mess
}
listOfdfChromSize[[i]]<-NA
}
} # end for for (i in 1:length(listOfdfChromSize)) {
listOfdfChromSize<-listOfdfChromSize[!is.na(listOfdfChromSize)]
#
# rebuild with centromereSize
#
listOfdfChromSize <- lapply(listOfdfChromSize, function(x) makeCharCols(x) )
return(listOfdfChromSize)
}
##############
addChrSizeColumn<-function(listOfdfChromSize){
for ( i in 1:length(listOfdfChromSize)) {
if(inherits(listOfdfChromSize[[i]], "data.frame")) {
if(attr(listOfdfChromSize[[i]], "cenType")=="monocen"){
listOfdfChromSize[[i]]<-makeNumCols(listOfdfChromSize[[i]])
listOfdfChromSize[[i]]$chrSize<-listOfdfChromSize[[i]]$shortArmSize+listOfdfChromSize[[i]]$longArmSize
} # if
} # if
} # for
return(listOfdfChromSize)
}
################### ordering function
addNeworderColumn<-function(listOfdfChromSize,orderlist){
for (s in 1:length(listOfdfChromSize)){
if(inherits(listOfdfChromSize[[s]], "data.frame")) {
listOfdfChromSize[[s]]<-listOfdfChromSize[[s]][orderlist[[s]], ] # important THIS orders
listOfdfChromSize[[s]]$neworder<-1:nrow(listOfdfChromSize[[s]])
}
} # end for
return(listOfdfChromSize)
}
###################
addAttributesDfChrSizeSimple <- function(listOfdfChromSize,centromereSize=NA,threshold=35, mymessage=TRUE){
for (i in 1:length(listOfdfChromSize)) {
#
# remove columns without info. per karyotype
#
listOfdfChromSize[[i]][listOfdfChromSize[[i]]==""]<-NA
listOfdfChromSize[[i]]<- listOfdfChromSize[[i]][, !apply(is.na(listOfdfChromSize[[i]]), 2, all)]
# Does the data.frame have short and long info?
if(mymessage){
message("\nChecking columns from dfChrSize\n" ) # mess
}
#################################################################################################
#
# let see if it is monocen
#
if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ) {
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste("\nOTU ",names(listOfdfChromSize)[[i]],"has all columns with info to have monocen. If not, you have to clean your data"))
)# message
}
attr(listOfdfChromSize[[i]],'cenType') <- "monocen"
#
# if larger than 100 000 reduce
#
myn<-max(pmax(listOfdfChromSize[[i]]$longArmSize+listOfdfChromSize[[i]]$shortArmSize) )
exp<-floor(log(myn , base = 10 ) )
divisor2<-10^exp
threshold2<- threshold/10
divisor2<-ifelse((myn/divisor2)<threshold2,divisor2<-10^(exp-1),divisor2)
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
# listOfdfChromSize[[i]]$longArmSize <- listOfdfChromSize[[i]]$longArmSize /divisor2
# listOfdfChromSize[[i]]$shortArmSize<- listOfdfChromSize[[i]]$shortArmSize/divisor2
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
attr(listOfdfChromSize[[i]],"centromere") <- centromereSize2 #/divisor2
listOfdfChromSize[[i]]$centromereSize <- centromereSize2 #/divisor2
} # if monocen success
##############################################################################################3
# let see if it is holocen
#
else if(length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )==0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," has all columns with info to have holocen. If not, you have to clean your data")))
) # message
}
attr(listOfdfChromSize[[i]], 'cenType') <- "holocen"
#
# if larger than 100 000 reduce
#
myn<-max(listOfdfChromSize[[i]]$chrSize)
exp<-floor(log(myn , base = 10 ) )
divisor2 <- 10^exp
threshold2 <- threshold/10
ifelse( (myn/divisor2)<threshold2, divisor2<-10^(exp-1) ,divisor2)
attr(listOfdfChromSize[[i]],"divisor") <- divisor2
# listOfdfChromSize[[i]]$chrSize <- listOfdfChromSize[[i]]$chrSize/divisor2
if(!is.na(centromereSize)){
centromereSize2<-centromereSize
} else {
centromereSize2<-divisor2
}
attr(listOfdfChromSize[[i]],"centromere") <- centromereSize2#/divisor2
listOfdfChromSize[[i]]$centromereSize <- centromereSize2#/divisor2
} # if holocen success
#
# let see if it is not monocen
#
else if(length( setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. with cen.: \nchrName, shortArmSize,longArmSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU ",names(listOfdfChromSize)[[i]]," does not have all columns with info to make a monocen.: ",
paste0(c(setdiff(c("chrName", "shortArmSize","longArmSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)) # pas
) # crayon
) # message
}
listOfdfChromSize[[i]]<-NA
} # fi
#
# let see if it is not holocen
#
else if (length( setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]]) ) )>0 ){
if(mymessage){
message("\nChecking mandatory columns from dfChrSize for chr. without cen.: \nchrName, chrSize,\n (column OTU is necessary if more than one species)\n"
) # mess
message(crayon::green(paste(c("\nOTU",names(listOfdfChromSize)[[i]],"does not have all columns with info to make a holocen:",
paste0(c(setdiff(c("chrName", "chrSize"),
colnames(listOfdfChromSize[[i]])
)," will be removed" # setdiff
), collapse = " "
) # paste
)))
) #mess
}
listOfdfChromSize[[i]]<-NA
}
} # end for for (i in 1:length(listOfdfChromSize)) {
listOfdfChromSize<-listOfdfChromSize[!is.na(listOfdfChromSize)]
#
# rebuild with centromereSize
#
listOfdfChromSize <- lapply(listOfdfChromSize, function(x) makeCharCols(x) )
return(listOfdfChromSize)
}
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