space converted into dots in header name
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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(readxl)
library(corrplot)
library("PerformanceAnalytics")
library("Hmisc")
library(psych)

list.files()
A <- read.table("Spearman.count.FINAL.txt",header=T, sep="\t",check.names=F)
# 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
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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.

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

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hello rpolicastro ,

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

Thanks,

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

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

Thanks,

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

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

Thanks,

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