hello
I work on microbiome data, I hope to know how to make a correlation between taxa (taxa at both axis) and plot the heatmap?
I think you want to use the corrplot package. Below I invented some data and plotted something similar to the image in your post.
MAT <- matrix(runif(100), nrow = 10)
dimnames(MAT) <- list(1:10, LETTERS[1:10])
MAT
#> A B C D E F
#> 1 0.951871830 0.4707230 0.24012347 0.5178127 0.2751222 0.65647700
#> 2 0.766769950 0.4421385 0.72756865 0.6000250 0.6886033 0.08601883
#> 3 0.647124767 0.6931287 0.26635338 0.2746420 0.7660176 0.48235816
#> 4 0.499733644 0.9299283 0.42957249 0.1024356 0.2939042 0.52092845
#> 5 0.970613548 0.5735708 0.05879489 0.8314679 0.8373080 0.69686842
#> 6 0.008677355 0.4761688 0.17473159 0.1486382 0.1598893 0.54540963
#> 7 0.324621430 0.8799219 0.32655718 0.3784643 0.7283856 0.30937435
#> 8 0.073627392 0.7993703 0.16689176 0.3884813 0.8852432 0.03588564
#> 9 0.983724692 0.6937437 0.87019572 0.6012237 0.8342834 0.94695733
#> 10 0.293158099 0.9222931 0.60094841 0.6124042 0.3541667 0.33163832
#> G H I J
#> 1 0.09200775 0.76309546 0.13565620 0.37810932
#> 2 0.15180410 0.75461615 0.08698062 0.31700478
#> 3 0.76680345 0.05135721 0.26739959 0.51625269
#> 4 0.87011836 0.30710263 0.92486552 0.01055717
#> 5 0.29454072 0.20666723 0.71695770 0.54783177
#> 6 0.98862719 0.76485283 0.92898327 0.16165668
#> 7 0.23338760 0.93043452 0.53492993 0.19314480
#> 8 0.37142818 0.04864177 0.04366780 0.20415356
#> 9 0.07701437 0.75130079 0.91461568 0.84231710
#> 10 0.03610030 0.58653198 0.46372324 0.07806065
CorMat <- cor(MAT, MAT)
corrplot::corrplot(CorMat, method = "color")
Created on 2019-11-08 by the reprex package (v0.3.0.9000)
Thank you i know understand how the correlation plot is drawn
My data resemble that data, i fallowed the instruction of corrplot package, i get a correlation between data of columns(as you illustrated) but i want to make a correlation between data of raws
I have 100taxa(100raws) and 22column
I would transpose the matrix with the t() function.
MAT <- matrix(runif(100), nrow = 10)
dimnames(MAT) <- list(LETTERS[1:10], 1:10)
head(MAT)
#> 1 2 3 4 5 6 7
#> A 0.18892224 0.30293810 0.6510487 0.3393431 0.3139483 0.66755333 0.8467336
#> B 0.12822771 0.88616629 0.1048321 0.3604074 0.2906694 0.34858701 0.1845633
#> C 0.66257674 0.96237661 0.4913882 0.2630195 0.3568480 0.14047893 0.6336629
#> D 0.08658182 0.52588874 0.6831611 0.1584937 0.3575360 0.01207774 0.2514396
#> E 0.44963824 0.24389143 0.2422095 0.2968011 0.2788004 0.48631095 0.7054812
#> F 0.30115486 0.01686491 0.4021860 0.6360747 0.7782060 0.78056557 0.4583389
#> 8 9 10
#> A 0.07322192 0.02385816 0.1008142
#> B 0.45646487 0.30320813 0.8876987
#> C 0.16846586 0.60985360 0.4392490
#> D 0.77025538 0.53005229 0.8712427
#> E 0.35058374 0.32530025 0.8128966
#> F 0.10074519 0.96814106 0.7126357
MAT_trans <- t(MAT)
head(MAT_trans)
#> A B C D E F G
#> 1 0.1889222 0.1282277 0.6625767 0.08658182 0.4496382 0.30115486 0.7975012
#> 2 0.3029381 0.8861663 0.9623766 0.52588874 0.2438914 0.01686491 0.5838637
#> 3 0.6510487 0.1048321 0.4913882 0.68316112 0.2422095 0.40218605 0.4272772
#> 4 0.3393431 0.3604074 0.2630195 0.15849372 0.2968011 0.63607473 0.9133669
#> 5 0.3139483 0.2906694 0.3568480 0.35753603 0.2788004 0.77820598 0.2557590
#> 6 0.6675533 0.3485870 0.1404789 0.01207774 0.4863110 0.78056557 0.8963948
#> H I J
#> 1 0.58418574 0.5788821 0.47426550
#> 2 0.47522843 0.4997649 0.51553313
#> 3 0.40586512 0.2824922 0.28249560
#> 4 0.88193416 0.6029224 0.88035809
#> 5 0.01977297 0.1195198 0.55975278
#> 6 0.36951783 0.5678245 0.01702115
CorMat <- cor(MAT_trans, MAT_trans)
corrplot::corrplot(CorMat, method = "color")
Created on 2019-11-08 by the reprex package (v0.3.0.9000)
Very useful, i will try
Thank you
hello, I made it but there is a minor problem
I want to abbreviate the taxonomy name to only include (genus), not the full name. are there any command to do that or I must alter the file by myself
thank you
There are many functions for manipulating strings in R. One example is the stringr package that is part of the tidyverse. In the example below, I take a vector where each element is two words and I change it to keep only the first word of each element. The regular expression "^[:alpha:]+" means: "from the start of the text, look for one or more alphabetic characters". A space is not an alphabetic character, so the function searches up to the first space. Perhaps this will work for your needs.
library(stringr)
#> Warning: package 'stringr' was built under R version 3.5.3
NAMES <- c("Aera Mowaslkd", "Ciouc Lsieldkdfj", "Duionecd Ldfosd ")
NAMES <- str_extract(NAMES, "^[:alpha:]+")
NAMES
#> [1] "Aera" "Ciouc" "Duionecd"
Created on 2019-11-09 by the reprex package (v0.3.0.9000)
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