space converted into dots in header name
0
0
Entering edit mode
3 months ago
Bioinfonext ▴ 330

I am using the below code to read a tab-delimited file which has spaces in the header name and these spaces converted into dots while plotting with corrplot.

Could anyone please help how I can avoid space to dot conversion?

library(vegan)
library(phyloseq)
library(ggplot2)
library(magrittr)
library(dplyr)
library(reshape2)
library(RColorBrewer)

library(corrplot)
library("PerformanceAnalytics")
library("Hmisc")
library(psych)

list.files()
# Convert the first column to be row names
B <- A[, -1]
C <- data.frame(B, row.names=A$Sample) M = as.matrix(C) #View(M) #--------------------Calculate correlation matrix and p-value matrix------------------------# #-------------------------------------spearman---------------------------------------------# cor_5 <- rcorr(as.matrix(M),type=c("spearman")) r_mat <- cor_5$r
p_mat <- cor_5\$P
# Extract the r and p (only Euka vs Bac, no inner correlations e.g. bac-bac)
r = r_mat[1:9,10:191]
p = p_mat[1:9,10:191]
# Only consider the positive correlation (r>0)
r_0 = r*(r> 0 )


Many thanks

R Rstudio microbiome • 336 views
0
Entering edit mode

A general solution for keeping spaces is to put individual header names in quotation marks. Don't know if that will be helpful with this package.

0
Entering edit mode

At what step in your code are they getting converted from spaces to dots?

0
Entering edit mode

hello rpolicastro ,

Could you please help me how I can investigate this issue step by step?

Thanks,

0
Entering edit mode

Use, 'check.names = FALSE'' in read.twble function.

0
Entering edit mode

Nothing is working from all the above suggestions. I am not sure at which step, spaces are converted in dots.

Thanks,

0
Entering edit mode

Thank you all. I have resolved this problem by substituting dot with space in the end.

colnames(r_0) <- gsub("\\.", " ", colnames(r_0))


Thanks,