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Add missing vis.immunr_gini #341

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Add missing vis.immunr_gini #341

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35d35cf
Add missing vis.immunr_gini
pwwang Jan 7, 2023
7f6bdb6
Fix title and labels for vis.immunr_gini
pwwang Jan 7, 2023
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20 changes: 19 additions & 1 deletion R/vis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2234,7 +2234,7 @@ vis_bar <- function(.data, .by = NA, .meta = NA, .errorbars = c(0.025, 0.975), .
#'
#' @concept diversity
#'
#' @aliases vis.immunr_chao1 vis.immunr_dxx vis.immunr_rarefaction vis.immunr_div vis.immunr_ginisimp vis.immunr_invsimp vis.immunr_hill
#' @aliases vis.immunr_chao1 vis.immunr_dxx vis.immunr_rarefaction vis.immunr_div vis.immunr_gini vis.immunr_ginisimp vis.immunr_invsimp vis.immunr_hill
#' @description An utility function to visualise the output from \code{\link{repDiversity}}.
#'
#' @importFrom reshape2 melt
Expand Down Expand Up @@ -2368,6 +2368,24 @@ vis.immunr_div <- function(.data, .by = NA, .meta = NA,
)
}

#' @export
vis.immunr_gini <- function(.data, .by = NA, .meta = NA,
.errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
.points = TRUE, .test = TRUE, .signif.label.size = 3.5, ...) {
# repDiversity(..., .method = "gini") generates a matrix
.data = data.frame(Sample = rownames(.data), Value = .data[, 1])

vis_bar(
.data = .data, .by = .by, .meta = .meta,
.errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
.points = .points, .test = .test, .signif.label.size = .signif.label.size,
.defgroupby = "Sample", .grouping.var = "Group",
.labs = c(NA, "Gini coefficient"),
.title = "Gini coefficient", .subtitle = "Sample diversity estimation using the Gini coefficient",
.legend = NA, .leg.title = NA
)
}

#' @export
vis.immunr_ginisimp <- function(.data, .by = NA, .meta = NA,
.errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
Expand Down