Thank you for your time.
Here are my commands.
library(qiime2R)
library(tidyverse)
metadata55<-readr::read_tsv("D:/Qiime222/New_metadata55.tsv")
#> Rows: 21 Columns: 11
#> -- Column specification --------------------------------------------------------
#> Delimiter: "\t"
#> chr (3): SampleID, Treatment, Period
#> dbl (8): pH, Alkalinity_g CaCO3/kg, TAN(g N/kg), TVFAs_g/kg, TS, VS, daily_m...
#>
#> i Use `spec()` to retrieve the full column specification for this data.
#> i Specify the column types or set `show_col_types = FALSE` to quiet this message.
uwunifrac<-read_qza("D:/Qiime222/unweighted_unifrac_pcoa_results.qza")
shannon<-read_qza("D:/Qiime222/shannon_vector.qza")$data %>% rownames_to_column("SampleID")
uwunifrac$data$Vectors %>%
+ left_join(metadata55) %>%
+ left_join(shannon) %>%
+ ggplot(aes(x=PC1, y=PC2, color= 'Period > 4', shape = 'Treatment', size= shannon_entropy)) + geom_point(alpha=0.5)+ xlab(paste(round(100*uwunifrac$data$vectors[1],2),"%")) + ylab(paste("PC2: ", round(100*uwunifrac$data$vectors[2]), "%")) + theme_bw() + scale_shape_manual(values=c(17,1), name="Period") + scale_size_continuous(name="Shannon Diversity") + scale_color_discrete(name="Period") + ggtitle("Unweighted UniFrac") + stat_ellipse()
#> Error in auto_copy(x, y, copy = copy): argument "y" is missing, with no default
Created on 2021-11-23 by the reprex package (v2.0.1)
The command you suggested gave this
the columns for Period and Treatment has this
.
