Nothing
utils::globalVariables(c("Names", "scores"))
#' Plots results from `lefser` function
#'
#' `lefserPlot` function displays effect sizes for differentially expressed microorganisms
#' and whether they are more abundant in '0' or '1' sample group.
#'
#' @param df
#' Data frame produced by `lefser`.
#'
#' @param colors character(2) The two colors corresponding to class 0 and 1,
#' respectively. Defaults to `c("red", "forestgreen")`.
#'
#' @param trim.names If `TRUE` extracts the most specific taxonomic rank of organism.
#'
#' @return
#' Function returns plot of effect size scores produed by `lefser`.
#' Positive scores represent microorganisms with that are more abundant in class '1'.
#' Negative scores represent microorganisms with that are more abundant in class '0'.
#'
#' @export
#' @importFrom ggplot2 ggplot aes ylab theme element_blank element_text
#' @importFrom ggplot2 geom_bar coord_flip scale_fill_manual
#'
#' @examples
#' example("lefser")
#' lefserPlot(res_group)
lefserPlot <- function(df, colors = c("red", "forestgreen"),
trim.names = TRUE) {
df <- trunc(df, trim.names)
group <- ifelse(df$scores > 0, 1, 0)
df$group <- as.factor(group)
plt <-
ggplot(df, aes(reorder(Names, scores), scores)) + ylab("LDA SCORE (log 10)") +
theme(
axis.title.y = element_blank(),
axis.title.x = element_text(size = 11, face = "bold"),
axis.text.y = element_text(
vjust = 0.7,
size = 9,
face = "bold"
),
axis.text.x = element_text(
vjust = 0.7,
size = 9,
face = "bold"
),
plot.title = element_text(
hjust = 0.5,
size = 13,
face = "bold"
)
) +
geom_bar(stat = "identity", aes(fill = group)) +
scale_fill_manual(values = colors) +
coord_flip()
return(plt)
}
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