Plot only Q-Q from ANOVA

Hi, and welcome!

One way to do this is with qqPlot() in the cars package, although you do get an envelope to go with it.

From help(aov) first example

library(car)
#> Loading required package: carData
op <- options(contrasts = c("contr.helmert", "contr.poly"))
( npk.aov <- aov(yield ~ block + N*P*K, npk) )
#> Call:
#>    aov(formula = yield ~ block + N * P * K, data = npk)
#> 
#> Terms:
#>                    block        N        P        K      N:P      N:K
#> Sum of Squares  343.2950 189.2817   8.4017  95.2017  21.2817  33.1350
#> Deg. of Freedom        5        1        1        1        1        1
#>                      P:K Residuals
#> Sum of Squares    0.4817  185.2867
#> Deg. of Freedom        1        12
#> 
#> Residual standard error: 3.929447
#> 1 out of 13 effects not estimable
#> Estimated effects are balanced
summary(npk.aov)
#>             Df Sum Sq Mean Sq F value  Pr(>F)   
#> block        5  343.3   68.66   4.447 0.01594 * 
#> N            1  189.3  189.28  12.259 0.00437 **
#> P            1    8.4    8.40   0.544 0.47490   
#> K            1   95.2   95.20   6.166 0.02880 * 
#> N:P          1   21.3   21.28   1.378 0.26317   
#> N:K          1   33.1   33.14   2.146 0.16865   
#> P:K          1    0.5    0.48   0.031 0.86275   
#> Residuals   12  185.3   15.44                   
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
coefficients(npk.aov)
#> (Intercept)      block1      block2      block3      block4      block5 
#>  54.8750000   1.7125000   1.6791667  -1.8229167  -1.0137500   0.2950000 
#>          N1          P1          K1       N1:P1       N1:K1       P1:K1 
#>   2.8083333  -0.5916667  -1.9916667  -0.9416667  -1.1750000   0.1416667
qqPlot(npk.aov)

#> [1] 3 5

Created on 2019-11-03 by the reprex package (v0.3.0)

BTW: Notice that I've used a reproducible example, called a reprex, which always helps questions get more answers.

2 Likes