library(tidyverse) library(ggplot2) #install.packages("heatmap3") library(heatmap3) #install.packages("gplots") library(gplots) library(ggpubr) library(factoextra) library(dplyr) library(stats) library(FactoMineR) setwd("/nfs/users/rg/jcebria/220928_mergepeaks/H3K4me3/peaks_division/221107/results") #to do correlaiton map between replicates df<-read.csv("H3K4me3.R1.R2.matrix.after.QN.merged.tsv", sep="\t") fd=cov(df[,c(-1)]) fd=round(fd) heatmap(fd) cormat <- round(cor(df),2) library(reshape2) melted_cormat <- melt(cormat) head(melted_cormat) library(ggplot2) ggplot(data = melted_cormat, aes(x=Var1, y=Var2, fill=value)) + geom_tile() #to do a heatmap of the 0 and 1 matrices df<-read.csv("H3K4me3_mp_oe_abspres.tsv", sep="\t") fd=df[,c(-2,-1,-3,-4)] heatmap3(as.matrix(fd), # widens margins around plot col=c("black","red"), cexCol = 1.5, Colv = NA, Rowv = TRUE, labRow = NA, cexRow = 0.75, hclustfun= hclust, scale = "none", symm = FALSE) legend("topright", legend = c("Absent","Present"), col = c("black","red"), cex=1.5, bty = "n", pch =15, pt.cex = 2 ) #to do pca by contribution df<-read.csv("H3K4me3.matrix.after.QN.merged.tsv", sep="\t") fd=log res.pca <- prcomp(fd, scale = TRUE) fviz_pca_ind(res.pca, geom="text",col.ind="contrib") + scale_color_gradient2(low="white", mid="blue", high="red", midpoint=4) fviz_pca_ind(res.pca, geom=c("point","text"),col.ind="contrib",repel = TRUE) + scale_color_gradient2(low="white", mid="blue", high="red", midpoint=4) #to do FC en plan locuras fd=log2(df) fd$min=apply(fd, 1, FUN = min) fed=fd fed$AL3=fd$AL3-fed$min fed$AWP=fd$AWP-fed$min fed$ALP=fd$ALP-fed$min fed$EL3=fd$EL3-fed$min fed$EWP=fd$EWP-fed$min fed$ELP=fd$ELP-fed$min fed$LL3=fd$LL3-fed$min fed$LWP=fd$LWP-fed$min fed$LLP=fd$LLP-fed$min fed$WL3=fd$WL3-fed$min fed$WWP=fd$WWP-fed$min fed$WLP=fd$WLP-fed$min fede=fed[,c(1:12)] fede$rowindex=row.names(fede) federico=melt(fede) ggplot(federico, aes(x=rowindex, y=value, color=variable)) + geom_point() ggplot(federico, aes(x=rowindex, y=value, color=variable)) + geom_point() + geom_smooth(method=lm, aes(fill=variable)) #to do FC respectul L3 fd=log2(df) fed=fd fed$AL3=fd$AL3-fd$AL3 fed$AWP=fd$AWP-fd$AL3 fed$ALP=fd$ALP-fd$AL3 fed$EL3=fd$EL3-fd$EL3 fed$EWP=fd$EWP-fd$EL3 fed$ELP=fd$ELP-fd$EL3 fed$LL3=fd$LL3-fd$LL3 fed$LWP=fd$LWP-fd$LL3 fed$LLP=fd$LLP-fd$LL3 fed$WL3=fd$WL3-fd$WL3 fed$WWP=fd$WWP-fd$WL3 fed$WLP=fd$WLP-fd$WL3 ##################from the new matrix check if size and intensity what df<-read.csv("H3K4me3_mp_oe_abspres_nonrestricted_Pi.tsv", sep="\t") df <- df %>% mutate(mAL3=case_when(df$mAL3==0 ~ 0.0001,df$mAL3!=0~df$mAL3)) df <- df %>% mutate(mAWP=case_when(df$mAWP==0 ~ 0.0001,df$mAWP!=0~df$mAWP)) df <- df %>% mutate(mALP=case_when(df$mALP==0 ~ 0.0001,df$mALP!=0~df$mALP)) df <- df %>% mutate(mEL3=case_when(df$mEL3==0 ~ 0.0001,df$mEL3!=0~df$mEL3)) df <- df %>% mutate(mEWP=case_when(df$mEWP==0 ~ 0.0001,df$mEWP!=0~df$mEWP)) df <- df %>% mutate(mELP=case_when(df$mELP==0 ~ 0.0001,df$mELP!=0~df$mELP)) df <- df %>% mutate(mLL3=case_when(df$mLL3==0 ~ 0.0001,df$mLL3!=0~df$mLL3)) df <- df %>% mutate(mLWP=case_when(df$mLWP==0 ~ 0.0001,df$mLWP!=0~df$mLWP)) df <- df %>% mutate(mLLP=case_when(df$mLLP==0 ~ 0.0001,df$mLLP!=0~df$mLLP)) df <- df %>% mutate(mWL3=case_when(df$mWL3==0 ~ 0.0001,df$mWL3!=0~df$mWL3)) df <- df %>% mutate(mWWP=case_when(df$mWWP==0 ~ 0.0001,df$mWWP!=0~df$mWWP)) df <- df %>% mutate(mWLP=case_when(df$mWLP==0 ~ 0.0001,df$mWLP!=0~df$mWLP)) df$size=df$end-df$start df$max=apply(df[,c(17,28)], 1, FUN = max) df <- df %>% mutate(max_color=case_when( df$max >= 20 ~ ">=20", df$max <5 ~ "<5", df$max <20 & df$max>=5~"5<=x<20" )) ###from sero/one matrix df <- df %>% mutate(Antenna=case_when((df$AL3 >= 1 | df$AWP >= 1 | df$ALP >= 1) ~ "Antenna",(df$AL3 == 0 & df$AWP == 0 & df$ALP == 0) ~ "Absent")) df <- df %>% mutate(Eye=case_when((df$EL3 >= 1 | df$EWP >= 1 | df$ELP >= 1) ~ "Eye",(df$EL3 == 0 & df$EWP == 0 & df$ELP == 0) ~ "Absent")) df<-df%>%mutate(Leg=case_when((df$LL3>=1|df$LWP>=1|df$LLP>=1)~"Leg",(df$LL3==0&df$LWP==0&df$LLP==0)~"Absent")) df<-df%>%mutate(Wing=case_when((df$WL3>=1|df$WWP>=1|df$WLP>=1)~"Wing",(df$WL3==0&df$WWP==0&df$WLP==0)~"Absent")) df<-df%>%mutate(L3=case_when((df$WL3>=1|df$LL3>=1|df$EL3>=1|df$AL3>=1)~"L3",(df$WL3==0|df$LL3==0|df$EL3==0|df$AL3==0)~"Absent")) df<-df%>%mutate(WP=case_when((df$WWP>=1|df$LWP>=1|df$EWP>=1|df$AWP>=1)~"WP",(df$WWP==0|df$LWP==0|df$EWP==0|df$AWP==0)~"Absent")) df<-df%>%mutate(LP=case_when((df$WLP>=1|df$LLP>=1|df$ELP>=1|df$ALP>=1)~"LP",(df$WLP==0|df$LLP==0|df$ELP==0|df$ALP==0)~"Absent")) df <- df %>% mutate(tissue= case_when( (df$Antenna == "Antenna" & df$Eye == "Eye" & df$Leg == "Leg" & df$Wing == "Wing") ~ "Non-specific", (df$Antenna == "Antenna" & df$Eye == "Absent" & df$Leg == "Absent" & df$Wing == "Absent") ~ "Antenna", (df$Antenna == "Absent" & df$Eye == "Eye" & df$Leg == "Absent" & df$Wing == "Absent") ~ "Eye", (df$Antenna == "Absent" & df$Eye == "Absent" & df$Leg == "Leg" & df$Wing == "Absent") ~ "Leg", (df$Antenna == "Absent" & df$Eye == "Absent" & df$Leg == "Absent" & df$Wing == "Wing") ~ "Wing", (df$Antenna == "Antenna" & df$Eye == "Absent" & df$Leg == "Absent" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Absent" & df$Eye == "Eye" & df$Leg == "Absent" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Absent" & df$Eye == "Absent" & df$Leg == "Leg" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Absent" & df$Eye == "Eye" & df$Leg == "Leg" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Antenna" & df$Eye == "Absent" & df$Leg == "Leg" & df$Wing == "Absent") ~ "Other", (df$Antenna == "Antenna" & df$Eye == "Eye" & df$Leg == "Absent" & df$Wing == "Absent") ~ "Other", (df$Antenna == "Absent" & df$Eye == "Eye" & df$Leg == "Leg" & df$Wing == "Absent") ~ "Other", (df$Antenna == "Absent" & df$Eye == "Eye" & df$Leg == "Leg" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Antenna" & df$Eye == "Absent" & df$Leg == "Leg" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Antenna" & df$Eye == "Eye" & df$Leg == "Absent" & df$Wing == "Wing") ~ "Other", (df$Antenna == "Antenna" & df$Eye == "Eye" & df$Leg == "Leg" & df$Wing == "Absent") ~ "Other", (df$Antenna == "Absent" & df$Eye == "Absent" & df$Leg == "Absent" & df$Wing == "Absent") ~ "Other" )) df <- df %>% mutate(sod= case_when( (df$L3 == "L3" & df$WP == "WP" & df$LP == "LP") ~ "Non-specific", (df$L3 == "L3" & df$WP == "Absent" & df$LP == "Absent") ~ "L3", (df$L3 == "Absent" & df$WP == "WP" & df$LP == "Absent") ~ "WP", (df$L3 == "Absent" & df$WP == "Absent" & df$LP == "LP") ~ "LP", (df$L3 == "L3" & df$WP == "Absent" & df$LP == "LP") ~ "Other", (df$L3 == "Absent" & df$WP == "WP" & df$LP == "LP") ~ "Other", (df$L3 == "L3" & df$WP == "WP" & df$LP == "Absent") ~ "Other", (df$L3 == "Absent" & df$WP == "Absent" & df$LP == "Absent") ~ "Other" )) df <- df %>% mutate(groups= case_when( (df$tissue=="Non-specific" & df$sod=="Non-specific") ~ "Non-specific", ((df$tissue=="Antenna"|df$tissue=="Eye"|df$tissue=="Leg"|df$tissue=="Wing") & (df$sod=="Other")) ~ "TP", ((df$tissue=="Antenna"|df$tissue=="Eye"|df$tissue=="Leg"|df$tissue=="Wing") & (df$sod=="Non-specific")) ~ "TP", ((df$sod=="L3"|df$sod=="LP"|df$sod=="WP") & df$tissue=="Non-specific") ~ "SP", ((df$sod=="L3"|df$sod=="LP"|df$sod=="WP") & df$tissue=="Other") ~ "SP", ((df$tissue=="Antenna"|df$tissue=="Eye"|df$tissue=="Leg"|df$tissue=="Wing") & (df$sod=="L3"|df$sod=="LP"|df$sod=="WP")) ~ "TSP", ((df$sod=="Other" | df$sod=="Non-specific") & (df$tissue=="Other" | df$tissue=="Non-specific")) ~ "Other" )) df <- df %>% mutate(color_groups= case_when( df$groups=="Non-specific" ~ "#a9ba9d", df$groups=="Other" ~ "#ffd600", df$groups=="SP" ~ "#fe64b3", df$groups=="TP" ~ "#9fc5e8", df$groups=="TSP" ~ "#cc66ff")) df <- df %>% mutate(color_sod= case_when( df$sod=="Non-specific" ~ "#a9ba9d", df$sod=="Other" ~ "#ffd602", df$sod=="WP" ~ "#de1818", df$sod=="L3" ~ "#de6262", df$sod=="LP" ~ "#820101")) df <- df %>% mutate(num_sod= case_when( df$sod=="Non-specific" ~ 1, df$sod=="Other" ~ 2, df$sod=="WP" ~ 3, df$sod=="L3" ~ 4, df$sod=="LP" ~ 5)) df <- df %>% mutate(color_tissue= case_when( df$tissue=="Non-specific" ~ "#a9ba9d", df$tissue=="Other" ~ "#ffd602", df$tissue=="Antenna" ~ "#ed760e", df$tissue=="Eye" ~ "#01665e", df$tissue=="Leg" ~ "#e31a1c", df$tissue=="Wing" ~ "#377eb8")) ##446041","#ffd602","#ed760e","#01665e","#e31a1c","#377eb8" ###frompeakintensities df<-df%>%mutate(mAntenna=case_when((df$mAL3>=5|df$mAWP>=5|df$mALP>=5)~"Antenna",(df$mAL3<5&df$mAWP<5&df$mALP<5)~"Absent")) df<-df%>%mutate(mEye=case_when((df$mEL3>=5|df$mEWP>=5|df$mELP>=5)~"Eye",(df$mEL3<5&df$mEWP<5&df$mELP<5)~"Absent")) df<-df%>%mutate(mLeg=case_when((df$mLL3>=5|df$mLWP>=5|df$mLLP>=5)~"Leg",(df$mLL3<5&df$mLWP<5&df$mLLP<5)~"Absent")) df<-df%>%mutate(mWing=case_when((df$mWL3>=5|df$mWWP>=5|df$mWLP>=5)~"Wing",(df$mWL3<5&df$mWWP<5&df$mWLP<5)~"Absent")) df<-df%>%mutate(mL3=case_when((df$mWL3>=5|df$mLL3>=5|df$mEL3>=5|df$mAL3>=5)~"L3",(df$mWL3<5|df$mLL3<5|df$mEL3<5|df$mAL3<5)~"Absent")) df<-df%>%mutate(mWP=case_when((df$mWWP>=5|df$mLWP>=5|df$mEWP>=5|df$mAWP>=5)~"WP",(df$mWWP<5|df$mLWP<5|df$mEWP<5|df$mAWP<5)~"Absent")) df<-df%>%mutate(mLP=case_when((df$mWLP>=5|df$mLLP>=5|df$mELP>=5|df$mALP>=5)~"LP",(df$mWLP<5|df$mLLP<5|df$mELP<5|df$mALP<5)~"Absent")) df <- df %>% mutate(mtissue= case_when( (df$mAntenna == "Antenna" & df$mEye == "Eye" & df$mLeg == "Leg" & df$mWing == "Wing") ~ "Non-specific", (df$mAntenna == "Antenna" & df$mEye == "Absent" & df$mLeg == "Absent" & df$mWing == "Absent") ~ "Antenna", (df$mAntenna == "Absent" & df$mEye == "Eye" & df$mLeg == "Absent" & df$mWing == "Absent") ~ "Eye", (df$mAntenna == "Absent" & df$mEye == "Absent" & df$mLeg == "Leg" & df$mWing == "Absent") ~ "Leg", (df$mAntenna == "Absent" & df$mEye == "Absent" & df$mLeg == "Absent" & df$mWing == "Wing") ~ "Wing", (df$mAntenna == "Antenna" & df$mEye == "Absent" & df$mLeg == "Absent" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Absent" & df$mEye == "Eye" & df$mLeg == "Absent" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Absent" & df$mEye == "Absent" & df$mLeg == "Leg" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Absent" & df$mEye == "Eye" & df$mLeg == "Leg" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Antenna" & df$mEye == "Absent" & df$mLeg == "Leg" & df$mWing == "Absent") ~ "Other", (df$mAntenna == "Antenna" & df$mEye == "Eye" & df$mLeg == "Absent" & df$mWing == "Absent") ~ "Other", (df$mAntenna == "Absent" & df$mEye == "Eye" & df$mLeg == "Leg" & df$mWing == "Absent") ~ "Other", (df$mAntenna == "Absent" & df$mEye == "Eye" & df$mLeg == "Leg" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Antenna" & df$mEye == "Absent" & df$mLeg == "Leg" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Antenna" & df$mEye == "Eye" & df$mLeg == "Absent" & df$mWing == "Wing") ~ "Other", (df$mAntenna == "Antenna" & df$mEye == "Eye" & df$mLeg == "Leg" & df$mWing == "Absent") ~ "Other", (df$mAntenna == "Absent" & df$mEye == "Absent" & df$mLeg == "Absent" & df$mWing == "Absent") ~ "Other" )) df <- df %>% mutate(msod= case_when( (df$mL3 == "L3" & df$mWP == "WP" & df$mLP == "LP") ~ "Non-specific", (df$mL3 == "L3" & df$mWP == "Absent" & df$mLP == "Absent") ~ "L3", (df$mL3 == "Absent" & df$mWP == "WP" & df$mLP == "Absent") ~ "WP", (df$mL3 == "Absent" & df$mWP == "Absent" & df$mLP == "LP") ~ "LP", (df$mL3 == "L3" & df$mWP == "Absent" & df$mLP == "LP") ~ "Other", (df$mL3 == "Absent" & df$mWP == "WP" & df$mLP == "LP") ~ "Other", (df$mL3 == "L3" & df$mWP == "WP" & df$mLP == "Absent") ~ "Other", (df$mL3 == "Absent" & df$mWP == "Absent" & df$mLP == "Absent") ~ "Other" )) df <- df %>% mutate(mgroups= case_when( (df$mtissue=="Non-specific" & df$msod=="Non-specific") ~ "Non-specific", ((df$mtissue=="Antenna"|df$mtissue=="Eye"|df$mtissue=="Leg"|df$mtissue=="Wing") & (df$msod=="Other")) ~ "TP", ((df$mtissue=="Antenna"|df$mtissue=="Eye"|df$mtissue=="Leg"|df$mtissue=="Wing") & (df$msod=="Non-specific")) ~ "TP", ((df$msod=="L3"|df$msod=="LP"|df$msod=="WP") & df$mtissue=="Non-specific") ~ "SP", ((df$msod=="L3"|df$msod=="LP"|df$msod=="WP") & df$mtissue=="Other") ~ "SP", ((df$mtissue=="Antenna"|df$mtissue=="Eye"|df$mtissue=="Leg"|df$mtissue=="Wing") & (df$msod=="L3"|df$msod=="LP"|df$msod=="WP")) ~ "TSP", ((df$msod=="Other" | df$msod=="Non-specific") & (df$mtissue=="Other" | df$mtissue=="Non-specific")) ~ "Other" )) #######plotar ggplot(df, aes(x=size,y=max,color=mgroups)) + geom_point() ggplot(df, aes(x=max,color=max_color)) + geom_density() ggplot(df, aes(x=size,color=groups)) + geom_density() ggplot(df, aes(size, after_stat(count), fill = max_color)) + geom_density(position = "fill") ggplot(df, aes(x=size,fill=max_color)) + geom_histogram(binwidth = 100 ) ggplot(df, aes(x=mgroups,fill=mgroups)) + geom_bar() RowSideColors<-df$color_tissue heatmap3(as.matrix(fd[,c(1:12,14)]),col=c("black","red"),Colv=TRUE,Rowv=NA,margins=c(2,10),RowSideColors=RowSideColors, legendfun=function() showLegend(legend=c("Non-specific","Other","TSP","TP","SP"),col=c("#a9ba9d","#ffd602","#cc66ff","#9fc5e8","#fe64b3"),cex=1.5)) RowSideColors<-df$color_tissue heatmap3(as.matrix(fd[,c(1:12,14)]),col=c("black","red"),Colv=TRUE,Rowv=NA,margins=c(2,10),RowSideColors=RowSideColors, legendfun=function() showLegend(legend=c("Non-specific","Other","Antenna","Eye","Leg","Wing"),col=c("#a9ba9d","#ffd602","#ed760e","#01665e","#e31a1c","#377eb8"),cex=1.5)) RowSideColors<-df$color_sod heatmap3(as.matrix(fd[,c(1:12,14)]),col=c("black","red"),Colv=TRUE,Rowv=df$sod,margins=c(2,10),RowSideColors=RowSideColors, legendfun=function() showLegend(legend=c("Non-specific","Other","WP","L3","LP"),col=c("#a9ba9d","#ffd602","#de1818","#de6262","#820101"),cex=1.5)) df$mean=apply(df[,c(17:28)], 1, FUN = mean) df$min=apply(df[,c(17:28)], 1, FUN = min) df$fcAL3=df$mAL3/df$mAL3 df$fcAWP=df$mAWP/df$mAL3 df$fcALP=df$mALP/df$mAL3 df$fcEL3=df$mEL3/df$mEL3 df$fcEWP=df$mEWP/df$mEL3 df$fcELP=df$mELP/df$mEL3 df$fcLL3=df$mLL3/df$mLL3 df$fcLWP=df$mLWP/df$mLL3 df$fcLLP=df$mLLP/df$mLL3 df$fcWL3=df$mWL3/df$mWL3 df$fcWWP=df$mWWP/df$mWL3 df$fcWLP=df$mWLP/df$mWL3 df$logAL3=abs(log2(df$fcAL3)) df$logAWP=abs(log2(df$fcAWP)) df$logALP=abs(log2(df$fcALP)) df$logEL3=abs(log2(df$fcEL3)) df$logEWP=abs(log2(df$fcEWP)) df$logELP=abs(log2(df$fcELP)) df$logLL3=abs(log2(df$fcLL3)) df$logLWP=abs(log2(df$fcLWP)) df$logLLP=abs(log2(df$fcLLP)) df$logWL3=abs(log2(df$fcWL3)) df$logWWP=abs(log2(df$fcWWP)) df$logWLP=abs(log2(df$fcWLP)) df<-df%>%mutate(logAntenna=case_when((df$logAL3>=1|df$logAWP>=1|df$logALP>=1)~"Antenna",(df$logAL3<1&df$logAWP<1&df$logALP<1)~"Absent")) df<-df%>%mutate(logEye=case_when((df$logEL3>=1|df$logEWP>=1|df$logELP>=1)~"Eye",(df$logEL3<1&df$logEWP<1&df$logELP<1)~"Absent")) df<-df%>%mutate(logLeg=case_when((df$logLL3>=1|df$logLWP>=1|df$logLLP>=1)~"Leg",(df$logLL3<1&df$logLWP<1&df$logLLP<1)~"Absent")) df<-df%>%mutate(logWing=case_when((df$logWL3>=1|df$logWWP>=1|df$logWLP>=1)~"Wing",(df$logWL3<1&df$logWWP<1&df$logWLP<1)~"Absent")) df<-df%>%mutate(logL3=case_when((df$logWL3>=1|df$logLL3>=1|df$logEL3>=1|df$logAL3>=1)~"L3",(df$logWL3<1|df$logLL3<1|df$logEL3<1|df$logAL3<1)~"Absent")) df<-df%>%mutate(logWP=case_when((df$logWWP>=1|df$logLWP>=1|df$logEWP>=1|df$logAWP>=1)~"WP",(df$logWWP<1|df$logLWP<1|df$logEWP<1|df$logAWP<1)~"Absent")) df<-df%>%mutate(logLP=case_when((df$logWLP>=1|df$logLLP>=1|df$logELP>=1|df$logALP>=1)~"LP",(df$logWLP<1|df$logLLP<1|df$logELP<1|df$logALP<1)~"Absent")) df <- df %>% mutate(logtissue= case_when( (df$logAntenna == "Antenna" & df$logEye == "Eye" & df$logLeg == "Leg" & df$logWing == "Wing") ~ "Non-specific", (df$logAntenna == "Antenna" & df$logEye == "Absent" & df$logLeg == "Absent" & df$logWing == "Absent") ~ "Antenna", (df$logAntenna == "Absent" & df$logEye == "Eye" & df$logLeg == "Absent" & df$logWing == "Absent") ~ "Eye", (df$logAntenna == "Absent" & df$logEye == "Absent" & df$logLeg == "Leg" & df$logWing == "Absent") ~ "Leg", (df$logAntenna == "Absent" & df$logEye == "Absent" & df$logLeg == "Absent" & df$logWing == "Wing") ~ "Wing", (df$logAntenna == "Antenna" & df$logEye == "Absent" & df$logLeg == "Absent" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Absent" & df$logEye == "Eye" & df$logLeg == "Absent" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Absent" & df$logEye == "Absent" & df$logLeg == "Leg" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Absent" & df$logEye == "Eye" & df$logLeg == "Leg" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Antenna" & df$logEye == "Absent" & df$logLeg == "Leg" & df$logWing == "Absent") ~ "Other", (df$logAntenna == "Antenna" & df$logEye == "Eye" & df$logLeg == "Absent" & df$logWing == "Absent") ~ "Other", (df$logAntenna == "Absent" & df$logEye == "Eye" & df$logLeg == "Leg" & df$logWing == "Absent") ~ "Other", (df$logAntenna == "Absent" & df$logEye == "Eye" & df$logLeg == "Leg" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Antenna" & df$logEye == "Absent" & df$logLeg == "Leg" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Antenna" & df$logEye == "Eye" & df$logLeg == "Absent" & df$logWing == "Wing") ~ "Other", (df$logAntenna == "Antenna" & df$logEye == "Eye" & df$logLeg == "Leg" & df$logWing == "Absent") ~ "Other", (df$logAntenna == "Absent" & df$logEye == "Absent" & df$logLeg == "Absent" & df$logWing == "Absent") ~ "Other" )) df <- df %>% mutate(logsod= case_when( (df$logL3 == "L3" & df$logWP == "WP" & df$logLP == "LP") ~ "Non-specific", (df$logL3 == "L3" & df$logWP == "Absent" & df$logLP == "Absent") ~ "L3", (df$logL3 == "Absent" & df$logWP == "WP" & df$logLP == "Absent") ~ "WP", (df$logL3 == "Absent" & df$logWP == "Absent" & df$logLP == "LP") ~ "LP", (df$logL3 == "L3" & df$logWP == "Absent" & df$logLP == "LP") ~ "Other", (df$logL3 == "Absent" & df$logWP == "WP" & df$logLP == "LP") ~ "Other", (df$logL3 == "L3" & df$logWP == "WP" & df$logLP == "Absent") ~ "Other", (df$logL3 == "Absent" & df$logWP == "Absent" & df$logLP == "Absent") ~ "Other" )) df <- df %>% mutate(loggroups= case_when( (df$logtissue=="Non-specific" & df$logsod=="Non-specific") ~ "Non-specific", ((df$logtissue=="Antenna"|df$logtissue=="Eye"|df$logtissue=="Leg"|df$logtissue=="Wing") & (df$logsod=="Other")) ~ "TP", ((df$logtissue=="Antenna"|df$logtissue=="Eye"|df$logtissue=="Leg"|df$logtissue=="Wing") & (df$logsod=="Non-specific")) ~ "TP", ((df$logsod=="L3"|df$logsod=="LP"|df$logsod=="WP") & df$logtissue=="Non-specific") ~ "SP", ((df$logsod=="L3"|df$logsod=="LP"|df$logsod=="WP") & df$logtissue=="Other") ~ "SP", ((df$logtissue=="Antenna"|df$logtissue=="Eye"|df$logtissue=="Leg"|df$logtissue=="Wing") & (df$logsod=="L3"|df$logsod=="LP"|df$logsod=="WP")) ~ "TSP", ((df$logsod=="Other" | df$logsod=="Non-specific") & (df$logtissue=="Other" | df$logtissue=="Non-specific")) ~ "Other" )) df <- df %>% mutate(Antenna_L3=case_when((df$logAL3 >=1) ~ 1,(df$logAL3 <1) ~ 0)) df <- df %>% mutate(Antenna_WP=case_when((df$logAWP >=1) ~ 2,(df$logAWP <1) ~ 0)) df <- df %>% mutate(Antenna_LP=case_when((df$logALP >=1) ~ 4,(df$logALP <1) ~ 0)) df <- df %>% mutate(Eye_L3=case_when((df$logEL3 >=1) ~ 8,(df$logEL3 <1) ~ 0)) df <- df %>% mutate(Eye_WP=case_when((df$logEWP >=1) ~ 16,(df$logEWP <1) ~ 0)) df <- df %>% mutate(Eye_LP=case_when((df$logELP >=1) ~ 32,(df$logELP <1) ~ 0)) df <- df %>% mutate(Leg_L3=case_when((df$logLL3 >=1) ~ 64,(df$logLL3 <1) ~ 0)) df <- df %>% mutate(Leg_WP=case_when((df$logLWP >=1) ~ 128,(df$logLWP <1) ~ 0)) df <- df %>% mutate(Leg_LP=case_when((df$logLLP >=1) ~ 256,(df$logLLP <1) ~ 0)) df <- df %>% mutate(Wing_L3=case_when((df$logWL3 >=1) ~ 512,(df$logWL3 <1) ~ 0)) df <- df %>% mutate(Wing_WP=case_when((df$logWWP >=1) ~ 1024,(df$logWWP <1) ~ 0)) df <- df %>% mutate(Wing_LP=case_when((df$logWLP >=1) ~ 2048,(df$logWLP <1) ~ 0)) df$sum=rowSums(df[,c(88:99)]) df <- df %>% mutate(num_groups=case_when( (df$sum==1|df$sum==2|df$sum==4|df$sum==8|df$sum==16|df$sum==32|df$sum==64|df$sum==128|df$sum==256|df$sum==512|df$sum==1024|df$sum==2048)~ "TSP", (df$sum==2340 | df$sum==585 | df$sum==1170 )~ "SP", (df$sum==7 | df$sum==56 |df$sum==448|df$sum==3584)~"TP", (df$sum==4096)~"Non-specific", (df$sum!=4096&df$sum!=7 & df$sum!=56 &df$sum!=448&df$sum!=3584&df$sum!=2340 & df$sum!=585 & df$sum!=1170&df$sum!=1&df$sum!=2&df$sum!=4&df$sum!=8&df$sum!=16&df$sum!=32&df$sum!=64&df$sum!=128&df$sum!=256&df$sum!=512&df$sum!=1024&df$sum!=2048)~ "Others" ))