I followed the post related to PCA from vcf file followed by
library("SNPRelate")
vcf.fn<-"~/xxx/tmp.vcf"
snpgdsVCF2GDS(vcf.fn, "ccm.gds", method="biallelic.only")
genofile <- openfn.gds("ccm.gds")
ccm_pca<-snpgdsPCA(genofile)
plot(ccm_pca$eigenvect[,1],ccm_pca$eigenvect[,2] ,col=as.numeric(substr(ccm_pca$sample, 1,3) == 'CCM')+3, pch=2)
I got a plot but not able to conclude from it. There is no legend or color code differentiation between the breeds. My understanding to R is very limited and couldn't able to find a fix. May I get some help/tips to fix this problem. I will be grateful to you all.
1 answer
I am confident that you know to what these numbers relate?
set specific colours for each factor level
You can set colours manually to any vector like this:
x <- c('01','03','05','01','08','08','01','03','05')
unique(x)
[1] "01" "03" "05" "08"
colours <- c('royalblue', 'forestgreen', 'red4', 'pink')[factor(x, levels = c('01', '03', '05', '08'))]
Here, the order of the colours ('royalblue', 'forestgreen', 'red4', 'pink') must match the order of the factor levels that you are setting ('01', '03', '05', '08').
apply a colour gradient / pre-built palette to your factor levels
You can also automatically assign colours via RColorBrewer:
require('RColorBrewer')
pick.col <- brewer.pal(10, 'Spectral')
colII <- colorRampPalette(pick.col)(length(unique(x)))[factor(x, levels = c('01', '03', '05', '08'))]
Here, I use the 'Spectral' palette. For other palettes, take a look here (half-way): http://www.sthda.com/english/wiki/colors-in-r
create your own palette
For a custom palette, do something like this:
myPalette <- c('white','pink','red2','red4')
colorRampPalette(myPalette)(length(unique(x)))[factor(x, levels = c('01', '03', '05', '08'))]
----------------------
You can then plot a custom legend via the legend() function, which comes with base R.
Kevin
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You are already attempting to set colours via this parameter:
Did you write this code (above) on your own?
What is the output of:
Dear Kevin, I found that code on previously mentioned post.
The output for
[1] "01" "03" "04" "05" "06"
[6] "07" "10:01" "10:03" "10:04" "10:05" [11] "10:06" "10:20" "20" "2:01" "2:03" [16] "2:04" "2:05" "2:06" "2:07" "2:20" [21] "3:01" "3:03" "3:04" "3:05" "3:06" [26] "3:07" "3:20" "4:01" "4:03" "4:04" [31] "4:05" "4:06" "4:07" "4:20" "5:01" [36] "5:03" "5:04" "5:05" "5:06" "5:07"
[1] "01" "03" "04" "05" "06" "07" "10:" [8] "10:" "10:" "10:" "10:" "10:" "20" "2:0" [15] "2:0" "2:0" "2:0" "2:0" "2:0" "2:2" "3:0" [22] "3:0" "3:0" "3:0" "3:0" "3:0" "3:2" "4:0" [29] "4:0" "4:0" "4:0" "4:0" "4:0" "4:2" "5:0" [36] "5:0" "5:0" "5:0" "5:0" "5:0
Respectively
Thanks for sharing..!!
Although this works perfectly I found one issue regarding grouping of samples manually. What if we have to color this group into forest green.
Similarly, this group into red color.
Any suggestion.
Is the
RedsorGreenspalette sufficient?Alternatively, you can literally use any colours that you want, like this: