Description Usage Details Author(s) References Examples

Option to plot individually all features found to be differentially presented in the classes of your dataset.

1 | ```
plots()
``` |

When executed, the name of the feature as well as the different output options will be prompted.

Alfonso Benitez-Paez

Benitez-Paez A. 2018. Permubiome: an R package to perform permutation based test for biomarker discovery in microbiome analyses. [https://cran.r-project.org]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | ```
## The function is currently defined as
function ()
{
Class<-NULL
loadNamespace("ggplot2")
load("permubiome.RData")
a <- array(, nrow(df_norm))
for (j in 1:nrow(df_norm)) {
a[j] <- sum(df_norm[j, 3:ncol(df_norm)])
}
for (l in 3:ncol(df_norm)) {
for (m in 1:nrow(df_norm)) {
df_norm[m, l] <- round((df_norm[m, l]/a[m]), digits = 6)
}
}
category <- readline("Type the category you want plotting : ")
if (category == "") {
category <- colnames(df_norm[3])
print(paste("As you declare no categories, the first one of your dataset is plotted!"))
}
else {
ggplot(df_norm, aes(Class, df_norm[, category]), environment = environment()) +
geom_boxplot(notch = F, outlier.colour = "blue",
outlier.shape = 1, outlier.size = 3, binaxis = "y",
stackdir = "center", dotsize = 3) + ggtitle(category) +
ylab("Normalized read proportion") + xlab("Classes") +
theme(axis.text = element_text(size = 12), axis.title = element_text(size = 16,
face = "bold")) + geom_jitter(position = position_jitter(width = 0,
height = 0))
output <- readline("Do you want an output file (yes/no)? : ")
if (substr(output, 1, 1) == "y") {
extension <- readline("What extension do you prefer fo the output plot
(ps, pdf, jpeg, tiff, png, bmp )? : ")
ggsave(filename = paste(category, extension, sep = "."),
plot = last_plot(), path = NULL, scale = 1, units = c("cm"),
dpi = 300, limitsize = TRUE)
}
else {
last_plot()
}
}
}
``` |

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