Here is my data (df called shannon_boxplot);
Samples Diversity
1 Control 3.309361
2 Control 3.664494
3 Control 3.269842
4 Disease 2.572888
5 Disease 1.530877
6 Disease 2.357401
dput(shannon_boxplot)
structure(list(Samples = structure(c(1L, 1L, 1L, 2L, 2L, 2L), .Label =
c("Control",
"Disease"), class = "factor"), Diversity = structure(c(5L, 6L,
4L, 3L, 1L, 2L), .Label = c("1.530877", "2.357401", "2.572888",
"3.269842", "3.309361", "3.664494"), class = "factor")), class =
"data.frame", row.names = c(NA,
-6L))
I am trying to plot a box plot to compare disease vs control. Here is the code that I have tried;
boxplot(Diversity ~ Samples, data=shannon_boxplot, xlab="Samples",
ylab="Shannon Diversity")
I am met with this error message Error in oldClass(stats) <- cl : adding class "factor" to an invalid object.
Using 1 for Controls and 2 for Disease in the sample column, gets the same error.
When I try and carry out a t test to compare the means of each group, I use this data;
shannon_diversity
Control1 3.309361
Control2 3.664494
Control3 3.269842
Disease1 2.572888
Disease2 1.530877
Disease3 2.357401
control_shannon <- shannon_divplot[1:3,1]
disease_shannon <- shannon_divplot[4:6,1]
ttest_out <- t.test(disease_shannon, control_shannon, alternative="two.sided", paired=F)$pvalue
I get the error message NULL with the above. Any help would be greatly appreciated. Thank-you