Adding t-test value to grouped data set in r

Question

When running stat_compare_means I am unable to run a t-test. If I leave the brackets empty it will attempt a Wilcoxen but I don't think it is accurate. I have tried editing several settings under stat_compare_means and tried changing to using geom_signif but have gotten a variety of different results.

Note: The data needs to be grouped this way as there are other groups I have left out.

#functions
se = function(x) {
  sd(x)/sqrt(length(x))
}

data_summary <- function(x) {
  m <- mean(x)
  ymin <- m-sd(x)
  ymax <- m+sd(x)
  return(c(y=m,ymin=ymin,ymax=ymax))
}

plot.mean <- function(x) {
  m <- mean(x)
  c(y = m, ymin = m, ymax = m)
}

#data set
HET.MOUSE.P
Mouse Brca1 Sex       Tx     Stage Count
 001  fl/+   M OLAPARIB AnnexinV+ 33.90
 002  fl/+   F     DMSO AnnexinV+ 44.20
 003   -/+   F OLAPARIB AnnexinV+ 40.00
 004   -/+   M     DMSO AnnexinV+ 32.60
 005   -/+   M OLAPARIB AnnexinV+ 34.80
 006   -/+   M OLAPARIB AnnexinV+ 21.82
 007  fl/+   F OLAPARIB AnnexinV+ 27.09
 008   -/+   F OLAPARIB AnnexinV+ 30.92
 009  fl/+   M     DMSO AnnexinV+  4.82
 010   -/+   M     DMSO AnnexinV+  3.97
 011   -/+   F     DMSO AnnexinV+  3.01
 012   -/+   F     DMSO AnnexinV+  2.91
 013   -/+   M     DMSO AnnexinV+  2.42
 014   -/+   M     DMSO AnnexinV+  4.15
 015   -/+   M OLAPARIB AnnexinV+  4.28

#plot code
HET.MOUSE.P.perT.med <- aggregate(Count ~ Stage + Tx, data = HET.MOUSE.P, median)
    HET.MOUSE.P.perT.med <- HET.MOUSE.P.perT.med %>%
      rename(med = Count)
    HET.MOUSE.P.perT.med
    HET.MOUSE.P.perT.se <- aggregate(Count ~ Stage + Tx, data = HET.MOUSE.P, se)
    HET.MOUSE.P.perT.se <- HET.MOUSE.P.perT.se %>%
      rename(se = Count)
    HET.MOUSE.P.perT.se
    
    HET.MOUSE.P.perT.simp <- merge(HET.MOUSE.P.perT.med, HET.MOUSE.P.perT.se)
    HET.MOUSE.P.perT.simp[is.na(HET.MOUSE.P.perT.simp)] <- 0
    HET.MOUSE.P.perT.simp  
    
    HET.MOUSE.P$Stage <-factor(HET.MOUSE.P$Stage)
    HET.MOUSE.P$Stage <-factor(HET.MOUSE.P$Stage, levels = c("AnnexinV+"))
    HET.MOUSE.P.perT.simp$Stage <-factor(HET.MOUSE.P.perT.simp$Stage, levels = c("AnnexinV+"))
   
    MOUSE.ttest <- compare_means(data = HET.MOUSE.P, Count~Tx, method = "t.test", paired = FALSE, group.by = "Stage")
     
     HET.MOUSE.P.perT.barplot = ggplot(HET.MOUSE.P.perT.simp, aes(x = Stage, y = med, fill = Tx)) +
      geom_bar(stat="identity", color="black", 
               position=position_dodge()) +
      geom_point(data = HET.MOUSE.P, aes(x = Stage, y = Count, fill = Tx), 
                 color = "white", pch=21, size= 3, position = position_dodge(width = .9), show.legend = FALSE) +
      geom_errorbar(aes(ymin = med, ymax=med+se), width=.2,
                    position=position_dodge(.9)) +
      scale_fill_manual(values = c("darkblue", "deepskyblue1")) +
      scale_shape_manual(values = c(0, 2)) +
      scale_x_discrete(limits=c("AnnexinV+")) +
      labs(x = NULL, y = "% Total Cells", fill ="Treatment", cex.lab = 5) +
      theme_classic() + ylim(0,50) +
      theme(text = element_text(family = "Arial"),
            plot.title = element_text(size = 16, hjust = 0.5, face = "bold"),
            axis.title.y = element_text(size = 12, face = "bold"),
            axis.text.x = element_text(size = 10, color = "black"), 
            axis.text.y = element_text(size = 14, color = "black"),
            axis.line = element_line(color = "Black"),
            legend.title = element_text(size = 11),
            legend.text = element_text(size = 11),
            legend.position = 'right',
            legend.justification = c(-0.05,-0.05)) +
       stat_compare_means(method = "t.test")

    HET.MOUSE.P.perT.barplot

After running this I get the error message:

Warning message: Computation failed in stat_compare_means(): Problem while computing p = purrr::map(...).

Adding t-test value to grouped data set in r

0 Answers0