[R] zigzag confidence interval in a plot

Dear All, When I plot the values and linear regression line for one data set, it is fine. But for another one I see zigzags, when I plot the confidence interval >cd Depth CHAOsep12RNA 9,94804 25,06 1476,83 40,04 1540,561404 50,11 1575,17 52,46 349,22 54,92 1941,5 57,2

[R] MANOVA summary.manova(m) :" residuals have rank"

Dear All, I am trying to perform MANOVA. I have table with 504 columns(species) and 36 rows) with two grouping (season and location) Zx <- Z[c(4:504)] Zxm <- as.matrix(Z) m<- manova(Zxm~Season*location, data=Z) when I do summary.aov, I get respond for each species but summary.manova summary.man

[R] vegan -varpart is bigger than 100% in total?

I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How i

Re: [R] spearman correlation and p-value as a matrix

aN  NaN  NaN >-0.61522514 >#3  NaN -0.89010286  NaN  NaN  NaN  NaN  NaN >-0.89010286 >#4  NaN  0.03036290  NaN  NaN  NaN  NaN  NaN  >0.03036290 >#5  NaN  0.08266317  NaN  NaN  NaN  NaN  NaN  >0.08266

Re: [R] spearman correlation and p-value as a matrix

resPnew<-as.matrix(resP[indx[,1],1]) > resrnew<-as.matrix(resr[indx[,1],1]) > >head(resPnew) >#  [,1] >#Otu00022_ag1 0.8047262 >#Otu00029_ag1   NaN >#Otu00039_ag1 0.8047262 >#Otu00042_ag1   NaN >#Otu00101_ag1 0.1583024 >#Otu00105_ag1   Na

[R] spearman correlation and p-value as a matrix

I have two data matrices that I want to make the correlation between each column from data1 and each column from data 2 and also calculate the p-value Matrices dont have the same size and I tried such a script. > bg <- read.table (file.choose(), header=T, row.names) > bg > Otu00022 Otu00029 Otu

[R] subsetting data file by intoducing a second file

Hello, I have a very data matrix and I have a file which has the names that I need to subset. However I cannot manage to subset the main file. ANy idea? bg <- read.table (file.choose(), header=T, row.names) bg Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu

[R] plot significant spearman correlation

Hello, I calculate the correlation between two matrices cor(x,y, method="spearman") and I am wondering if it possible to see only the significant correlations. I can do that for single OTUs with cor.test() command but I would like to have an output for whole matrix. Besides,I would like to plot

[R] ggplot zoomin

Dear All, I am plotting a graph in ggplot, I would like to magnify the values between 0-1 without losing data in the higher range. How can I do that? neither scale_y_continous nor coord_cartesian works. Thank you Özgül Université Libre de Bruxelles _

[R] labdsv-indval Windows GUI front-end stopped working.

Dear All, I have a problem with indval command. Last week, I could run it on my pc without any problem. Today, I tried to run the command "indval" and it constantly gives the error windows GUI front-end had stopped working, and it shuts the program. I was using 2.14.2 and I even uploaded new ve