I already solved this issue thank you so much for all ur help.
This is what I did, if you want to know.
library(vegan)
library(readxl)
#rarefy con la media de reads por muestra Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes - PMC
familia<- read_excel("~/RSTUDIO/Datos_cianobacterias/Cianobacterias_familia_sin3h5c.xlsx")
#columna con las muestrasias
data <- familia
replicates <- as.data.frame(colnames(data)[-1])
colnames(replicates) <- "replicates"
attach(familia)
rwnames <- index
data <- as.matrix(data[,-1])
estimateR(data)
ch <- estimateR(data)
ch=estimateR(data)[2,]
write.csv(ch, file = "~/RSTUDIO/Datos_cianobacterias/ch-estimater-familia.csv")
#boxplot
#agregar el Tx= Control MS o T2DM
bpdata <- read.csv("~/RSTUDIO/Datos_cianobacterias/Metadata-final-sin3h5c.csv", row.names=1)
attach(bpdata)
colvec<- c("yellowgreen","darkturquoise", "coral")
boxplot(ch~Month, bpdata, col = colvec, ylab = "Chao1", main = "Species Diversity")
library(ggplot2)
library(ggsignif)
res.aov =aov(ch ~ Month, data = bpdata)
summary(res.aov)#p-value<0.05
TukeyHSD(res.aov)
bpdata$Month <- factor(bpdata$Month,
labels = c("Jul", "Aug", "Sep"))
tumeans <- aggregate(ch ~ Month, bpdata, mean)
library(ggplot2)
library(ggsignif)
library(tidyverse)
bxplot <- ggplot(bpdata, aes(x=Month, y = ch, fill =Month )) +
geom_boxplot() +
geom_signif(comparisons = list(c("Jul", "Aug")),
map_signif_level=TRUE,
margin_top = 0.05)+
geom_signif(comparisons = list(c("Aug", "Sep")),
map_signif_level=TRUE,
margin_top = 0.15)+
geom_signif(comparisons = list(c("Jul", "Sep")),
map_signif_level=TRUE,
margin_top = 0.25)+
geom_boxplot(show.legend = FALSE) +
scale_y_continuous(expand = c(0.05,0.05))+
ggtitle("Chao1")+
theme_bw() +
theme(panel.grid.major = element_line(colour = "white"),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
plot.title = element_text(hjust = 0.5, size = 14, family = "Tahoma", face = "bold"),
text=element_text(family = "Tahoma"),
axis.title = element_text(face="bold"),
axis.text.x = element_text(colour="black", size = 11),
axis.text.y = element_text(colour="black", size = 9),
axis.line = element_line(size=0.5, colour = "black"))
scale_fill_brewer(palette = "Accent")
bxplot
Have a good day 