My guess is that the "%>% data.frame %>%" step turned something into a
character that you thought would be a factor.
See this example. Remember that the stringsAFactors argument to
data.frame was recently changed.
> tmp <- data.frame(A=c("A","F","B","G","C"), B=1:5, CC=6:10)
> tmp
A B CC
1 A 1 6
2 F 2 7
3 B 3 8
4 G 4 9
5 C 5 10
> sapply(tmp,class)
A B CC
"character" "integer" "integer"
> tmp[order(tmp$A),]
A B CC
1 A 1 6
3 B 3 8
5 C 5 10
2 F 2 7
4 G 4 9
> tmp$A <- factor(tmp$A, levels=unique(tmp$A))
> sapply(tmp,class)
A B CC
"factor" "integer" "integer"
> tmp[order(tmp$A),]
A B CC
1 A 1 6
2 F 2 7
3 B 3 8
4 G 4 9
5 C 5 10
>
On Fri, Nov 6, 2020 at 9:18 AM Ana Marija <sokovic.anamar...@gmail.com> wrote:
>
> sorry forgot to attach the plot.
>
> On Fri, Nov 6, 2020 at 8:07 AM Ana Marija <sokovic.anamar...@gmail.com> wrote:
> >
> > Hello
> >
> > I have data like this:
> >
> > > head(my_data)
> > subjects DIABDUR HBA1C ESRD SEX AGE PHENO C1 C2
> > 1 fam0110_G110 38 9.4 1 2 51 2 -0.01144980 0.002661140
> > 2 fam0113_G113 30 12.5 1 2 40 2 -0.00502052 -0.000929061
> > 3 fam0114_G114 23 8.4 2 2 45 2 -0.00251578 -0.003450950
> > 4 fam0117_G117 37 9.0 2 2 46 2 -0.00704917 -0.000573325
> > 5 fam0119_G119 22 9.4 1 1 46 1 0.00263433 0.001002370
> > 6 fam0119_G120 NA NA 1 1 71 1 -0.00354795 -0.002045940
> > C3 C4 C5 C6 C7 C8
> > 1 0.006028150 -0.00176795 -0.00148375 0.004543550 -0.006272170 -0.00535077
> > 2 -0.000453402 -0.00192162 0.00416229 0.007868230 -0.001957670 -0.00473148
> > 3 -0.001680860 -0.00620438 -0.00235092 0.000672831 -0.000278318 0.00647337
> > 4 0.001436740 0.00155568 -0.00556147 -0.000386401 -0.006885350 0.00135539
> > 5 -0.007396920 0.00326229 0.00355575 -0.011149400 0.009156510 0.00120833
> > 6 0.004532050 0.00869862 -0.00113207 0.002244520 -0.002119220 0.00657587
> > C9 C10
> > 1 0.00328111 -0.00113515
> > 2 -0.00495790 0.00320201
> > 3 0.00208591 -0.00874752
> > 4 -0.00967934 0.00607760
> > 5 0.00611030 0.00876190
> > 6 -0.00990661 0.00635349
> >
> > I am plotting it with:
> >
> > library(dplyr)
> > library(magrittr)
> > library(corrplot)
> > d=my_data %>% data.frame %>% set_rownames(.$subjects) %>% select(-subjects)
> > res <- cor(d, use = "complete.obs")
> > pdf("correlation.pdf")
> > corrplot(res, type = "upper", order = "hclust",
> > tl.col = "black", tl.srt = 45)
> > dev.off()
> >
> > and I am getting the plot in attach. How to make it so that my
> > variables are shown on the plot in the order they are in my_data data
> > frame?
> >
> > Thanks
> > Ana
> ______________________________________________
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