Comparing CCPs

Quick analysis of CCPs obtained using different methods on 100 families of Deltaproteobacteria.

setwd("/home/boussau/Data/TransferRelated/ComparisonCCPDavin/ComparisonCCPs")
d<-read.table("ComparisonCCDs.tsv", h=T)
summary(d)

           FM        IQDIST_D         IQDIST_L        IQDIST_LL          IQDIST_RD          IQDIST_RL       
 DELTA000004: 1   Min.   : 0.000   Min.   : 0.000   Min.   :-221.439   Min.   :0.000001   Min.   :0.000001  
 DELTA000110: 1   1st Qu.: 0.000   1st Qu.: 2.252   1st Qu.: -87.649   1st Qu.:0.000001   1st Qu.:0.057327  
 DELTA000139: 1   Median : 0.025   Median : 5.580   Median : -48.546   Median :0.001411   Median :0.165886  
 DELTA000170: 1   Mean   : 2.357   Mean   : 7.181   Mean   : -66.970   Mean   :0.097253   Mean   :0.202848  
 DELTA000341: 1   3rd Qu.: 3.110   3rd Qu.: 9.565   3rd Qu.: -29.078   3rd Qu.:0.097512   3rd Qu.:0.335495  
 DELTA000356: 1   Max.   :24.000   Max.   :43.360   Max.   :  -5.339   Max.   :1.025130   Max.   :0.633318  
 (Other)    :94                                                                                             
   IQDIST_RT           IQDIST_T       IQNEWDIST_D      IQNEWDIST_L      IQNEWDIST_LL       IQNEWDIST_RD     
 Min.   :0.000001   Min.   : 0.000   Min.   : 0.000   Min.   : 0.000   Min.   :-235.182   Min.   :0.000001  
 1st Qu.:0.023388   1st Qu.: 1.018   1st Qu.: 0.000   1st Qu.: 2.165   1st Qu.: -88.914   1st Qu.:0.000001  
 Median :0.076179   Median : 3.625   Median : 0.020   Median : 5.635   Median : -48.566   Median :0.002423  
 Mean   :0.103737   Mean   : 5.584   Mean   : 2.319   Mean   : 7.254   Mean   : -66.917   Mean   :0.097831  
 3rd Qu.:0.151390   3rd Qu.: 7.965   3rd Qu.: 3.105   3rd Qu.: 9.460   3rd Qu.: -29.093   3rd Qu.:0.097245  
 Max.   :0.493569   Max.   :24.400   Max.   :24.000   Max.   :36.410   Max.   :  -5.344   Max.   :1.025130  
                                                                                                            
  IQNEWDIST_RL       IQNEWDIST_RT       IQNEWDIST_T      PBCATDIST_D      PBCATDIST_L      PBCATDIST_LL     
 Min.   :0.000001   Min.   :0.000001   Min.   : 0.000   Min.   : 0.000   Min.   : 0.000   Min.   :-224.285  
 1st Qu.:0.058323   1st Qu.:0.026169   1st Qu.: 1.020   1st Qu.: 0.000   1st Qu.: 1.700   1st Qu.: -90.931  
 Median :0.172801   Median :0.069065   Median : 3.475   Median : 0.345   Median : 4.655   Median : -49.464  
 Mean   :0.205269   Mean   :0.098739   Mean   : 5.575   Mean   : 2.261   Mean   : 6.058   Mean   : -65.631  
 3rd Qu.:0.337602   3rd Qu.:0.154671   3rd Qu.: 7.800   3rd Qu.: 3.050   3rd Qu.: 8.535   3rd Qu.: -28.155  
 Max.   :0.635611   Max.   :0.441210   Max.   :28.160   Max.   :24.000   Max.   :30.860   Max.   :  -6.352  
                                                                                                            
  PBCATDIST_RD       PBCATDIST_RL       PBCATDIST_RT       PBCATDIST_T     PBLGCATDIST_D    PBLGCATDIST_L   
 Min.   :0.000001   Min.   :0.000001   Min.   :0.000001   Min.   : 0.000   Min.   : 0.000   Min.   : 0.000  
 1st Qu.:0.000001   1st Qu.:0.045078   1st Qu.:0.022838   1st Qu.: 1.040   1st Qu.: 0.000   1st Qu.: 1.950  
 Median :0.006233   Median :0.132756   Median :0.065688   Median : 4.110   Median : 0.000   Median : 4.365  
 Mean   :0.094619   Mean   :0.183016   Mean   :0.095169   Mean   : 5.058   Mean   : 2.234   Mean   : 6.093  
 3rd Qu.:0.085012   3rd Qu.:0.317036   3rd Qu.:0.134741   3rd Qu.: 7.497   3rd Qu.: 3.062   3rd Qu.: 8.357  
 Max.   :1.028940   Max.   :0.651366   Max.   :0.470747   Max.   :22.270   Max.   :24.000   Max.   :36.150  
                                                                                                            
 PBLGCATDIST_LL     PBLGCATDIST_RD      PBLGCATDIST_RL     PBLGCATDIST_RT     PBLGCATDIST_T   
 Min.   :-215.031   Min.   :0.0000010   Min.   :0.000001   Min.   :0.000001   Min.   : 0.000  
 1st Qu.: -81.391   1st Qu.:0.0000010   1st Qu.:0.043473   1st Qu.:0.025359   1st Qu.: 1.048  
 Median : -48.422   Median :0.0001322   Median :0.144134   Median :0.060798   Median : 3.280  
 Mean   : -63.497   Mean   :0.0934242   Mean   :0.187107   Mean   :0.092349   Mean   : 4.841  
 3rd Qu.: -28.306   3rd Qu.:0.0905567   3rd Qu.:0.320606   3rd Qu.:0.130447   3rd Qu.: 7.308  
 Max.   :  -5.402   Max.   :1.0207100   Max.   :0.623895   Max.   :0.449569   Max.   :22.690  
                                                                                              

Paired test on the number of transfers between IQ and IQ TEST

t.test(d$IQDIST_T, d$IQNEWDIST_T, paired = T)

    Paired t-test

data:  d$IQDIST_T and d$IQNEWDIST_T
t = 0.046398, df = 99, p-value = 0.9631
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -0.3466503  0.3632503
sample estimates:
mean of the differences 
                 0.0083 

Paired test on the number of transfers between PBCAT and IQ

t.test(d$PBCATDIST_T, d$IQDIST_T, paired = T)

    Paired t-test

data:  d$PBCATDIST_T and d$IQDIST_T
t = -2.5893, df = 99, p-value = 0.01107
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -0.9281945 -0.1228055
sample estimates:
mean of the differences 
                -0.5255 

Paired test on the LogLK between PBCAT and IQ

t.test(d$PBCATDIST_LL, d$IQDIST_LL, paired = T)

    Paired t-test

data:  d$PBCATDIST_LL and d$IQDIST_LL
t = 2.2792, df = 99, p-value = 0.0248
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 0.1733311 2.5053721
sample estimates:
mean of the differences 
               1.339352 

Paired test on the loglk between PBCAT and PBLG+CAT

t.test(d$PBCATDIST_LL, d$PBLGCATDIST_LL, paired = T)

    Paired t-test

data:  d$PBCATDIST_LL and d$PBLGCATDIST_LL
t = -3.5649, df = 99, p-value = 0.0005622
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -3.3215050 -0.9461504
sample estimates:
mean of the differences 
              -2.133828 

Paired test on the number of transfers between PBCAT and PBLG+CAT

t.test(d$PBCATDIST_T, d$PBLGCATDIST_T, paired = T)

    Paired t-test

data:  d$PBCATDIST_T and d$PBLGCATDIST_T
t = 1.4351, df = 99, p-value = 0.1544
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -0.08303086  0.51703086
sample estimates:
mean of the differences 
                  0.217 

Analysis on the 4 methods according to which gets the best loglk for each family

# Let's rank by the loglk
dll <- cbind(d$IQDIST_LL, d$IQNEWDIST_LL, d$PBCATDIST_LL, d$PBLGCATDIST_LL)
cols <- apply (dll, 1, function (x) {which(max(x)==x)} )
table(unlist(cols))

 1  2  3  4 
16 18 23 44 

In 44 cases, PBLG+CAT is best, then in 23 cases, PB+CAT is best, then in 18 cases IQ TEST is best, then in 16 cases IQ is best.

Graphical representation

# Add extra space to right of plot area; change clipping to figure
par(mar=c(5.1, 4.1, 4.1, 10.1), xpd=TRUE)
plot(1:length(unlist(cols)), unlist(cols), col=unlist(cols), ylab="Best gene tree according to ALE dated (logLk)", xlab="Delta proteobacteria family", pch=20)
legend("topright",inset=c(-0.3,0), c("IQ", "IQ TEST", "PB CAT", "PBLG+CAT"), pch = c(20,20,20,20), col = c(1,2,3,4))