diff --git a/R/Accumulation.R b/R/Accumulation.R index 7a1caaa..02912ca 100644 --- a/R/Accumulation.R +++ b/R/Accumulation.R @@ -237,9 +237,9 @@ autoplot.AccumCurve <- function(object, ..., main = NULL, xlab = "Sample Size", ylab = NULL, ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size) + col = "black", + lty = 1, + lwd = 0.5) { thePlot <- ggplot2::ggplot(as.data.frame.list(object), ggplot2::aes(x=.data$x, y=.data$y)) if (!(is.null(object$high) | is.null(object$low))) { diff --git a/R/CommunityProfile.R b/R/CommunityProfile.R index 9729b15..1aa336c 100644 --- a/R/CommunityProfile.R +++ b/R/CommunityProfile.R @@ -131,9 +131,9 @@ autoplot.CommunityProfile <- function(object, ..., main = NULL, xlab = "Order of Diversity", ylab = "Diversity", ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size) + col = "black", + lty = 1, + lwd = 0.5) { thePlot <- ggplot2::ggplot(as.data.frame.list(object), ggplot2::aes(x=.data$x, y=.data$y)) if (!(is.null(object$high) | is.null(object$low))) { diff --git a/R/DivPart.R b/R/DivPart.R index bb212e2..76c3b4a 100644 --- a/R/DivPart.R +++ b/R/DivPart.R @@ -93,8 +93,8 @@ function (x, ...) autoplot.DivPart <- -function (object, col = ggplot2::GeomRect$default_aes$fill, - border = ggplot2::GeomRect$default_aes$colour, ...) +function (object, col = "grey35", + border = NA, ...) { thePlot <- ggplot2::ggplot() + ggplot2::geom_rect(ggplot2::aes(xmin=.data$xmin, ymin=.data$ymin, xmax=.data$xmax, ymax=.data$ymax), diff --git a/R/DivProfile.R b/R/DivProfile.R index a564ea4..acb395f 100644 --- a/R/DivProfile.R +++ b/R/DivProfile.R @@ -219,9 +219,9 @@ function (x, ..., main = NULL, xlab = "Order of Diversity", ylab = NULL, Which = autoplot.DivProfile <- function (object, ..., main = NULL, xlab = "Order of Diversity", ylab = NULL, Which = "All", ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", labels = NULL, font.label = list(size=11, face="plain"), - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size) + col = "black", + lty = 1, + lwd = 0.5) { if (Which == "All" | (Which == "Alpha" & is.null(main))) main <- "Total Alpha Diversity" if (Which == "All" | (Which == "Alpha" & is.null(ylab))) ylab <- expression(paste(alpha, " diversity")) diff --git a/R/MCdiversity.R b/R/MCdiversity.R index affb211..c9dcff7 100644 --- a/R/MCdiversity.R +++ b/R/MCdiversity.R @@ -20,8 +20,8 @@ function (x, ...) autoplot.MCdiversity <- -function (object, col = ggplot2::GeomCol$default_aes$fill, - border = ggplot2::GeomCol$default_aes$colour, ...) +function (object, col = "grey35", + border = NA, ...) { theData <- data.frame(x=c(names(object$Communities), "", "Metacommunity"), y=c(object$Communities, 0, object$Total)) # Factors to keep the order of bars (avoid sort by name) diff --git a/R/MCentropy.R b/R/MCentropy.R index b24ba75..213adb7 100644 --- a/R/MCentropy.R +++ b/R/MCentropy.R @@ -19,8 +19,8 @@ function (x, ...) autoplot.MCentropy <- -function (object, col = ggplot2::GeomCol$default_aes$fill, - border = ggplot2::GeomCol$default_aes$colour, ...) +function (object, col = "grey35", + border = NA, ...) { theData <- data.frame(x=c(names(object$Communities), "", "Metacommunity"), y=c(object$Communities, 0, object$Total)) # Factors to keep the order of bars (avoid sort by name) diff --git a/R/PhyloValue.R b/R/PhyloValue.R index 9bdea6b..6943b78 100644 --- a/R/PhyloValue.R +++ b/R/PhyloValue.R @@ -33,9 +33,9 @@ function (x, xlab = expression(italic("T")), ylab = NULL, main = NULL, ...) autoplot.PhyloValue <- function (object, xlab = expression(italic("T")), ylab = NULL, main = NULL, - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size, + col = "black", + lty = 1, + lwd = 0.5, ...) { Entity <- "" diff --git a/R/SpeciesDistribution.R b/R/SpeciesDistribution.R index 3560eec..0916407 100644 --- a/R/SpeciesDistribution.R +++ b/R/SpeciesDistribution.R @@ -371,9 +371,9 @@ function(x, ..., Distribution = NULL, autoplot.SpeciesDistribution <- function(object, ..., Distribution = NULL, ylog = TRUE, main = NULL, xlab = "Rank", ylab = NULL, - pch = ggplot2::GeomPoint$default_aes$shape, - col = ggplot2::GeomPoint$default_aes$colour, - cex = ggplot2::GeomPoint$default_aes$size) + pch = 19, + col = "black", + cex = 1.5) { # Eliminate zeros and sort Ns <- sort(object[object > 0], decreasing = TRUE) diff --git a/man/Accumulation.Rd b/man/Accumulation.Rd index 01dbf35..adf2c78 100644 --- a/man/Accumulation.Rd +++ b/man/Accumulation.Rd @@ -27,9 +27,9 @@ DivAC(Ns, q = 0, n.seq = seq_len(sum(Ns)), PCorrection="Chao2015", Unveiling="ge \method{autoplot}{AccumCurve}(object, ..., main = NULL, xlab = "Sample Size", ylab = NULL, ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size) + col = "black", + lty = 1, + lwd = 0.5) } \arguments{ \item{x}{ diff --git a/man/CommunityProfile.Rd b/man/CommunityProfile.Rd index 654a396..6717bfd 100644 --- a/man/CommunityProfile.Rd +++ b/man/CommunityProfile.Rd @@ -23,9 +23,9 @@ is.CommunityProfile(x) \method{autoplot}{CommunityProfile}(object, \dots, main = NULL, xlab = "Order of Diversity", ylab = "Diversity", ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size) + col = "black", + lty = 1, + lwd = 0.5) CEnvelope(Profile, LineWidth = 2, ShadeColor = "grey75", BorderColor = "red", \dots) } \arguments{ diff --git a/man/DivPart.Rd b/man/DivPart.Rd index 3fb14f8..9635a6d 100644 --- a/man/DivPart.Rd +++ b/man/DivPart.Rd @@ -15,8 +15,8 @@ DivPart(q = 1, MC, Biased = TRUE, Correction = "Best", Tree = NULL, Normalize = TRUE, Z = NULL, CheckArguments = TRUE) is.DivPart(x) \method{plot}{DivPart}(x, \dots) -\method{autoplot}{DivPart}(object, col = ggplot2::GeomRect$default_aes$fill, - border = ggplot2::GeomRect$default_aes$colour, \dots) +\method{autoplot}{DivPart}(object, col = "grey35", + border = NA, \dots) \method{summary}{DivPart}(object, \dots) } \arguments{ diff --git a/man/DivProfile.Rd b/man/DivProfile.Rd index 79f8f4a..2e863b2 100644 --- a/man/DivProfile.Rd +++ b/man/DivProfile.Rd @@ -22,9 +22,9 @@ is.DivProfile(x) \method{autoplot}{DivProfile}(object, \dots, main = NULL, xlab = "Order of Diversity", ylab = NULL, Which = "All", ShadeColor = "grey75", alpha = 0.3, BorderColor = "red", labels = NULL, font.label = list(size=11, face="plain"), - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size) + col = "black", + lty = 1, + lwd = 0.5) \method{summary}{DivProfile}(object, \dots) } \arguments{ diff --git a/man/MCdiversity.Rd b/man/MCdiversity.Rd index cb3c6a9..3c4804a 100644 --- a/man/MCdiversity.Rd +++ b/man/MCdiversity.Rd @@ -13,8 +13,8 @@ \usage{ is.MCdiversity(x) \method{plot}{MCdiversity}(x, \dots) -\method{autoplot}{MCdiversity}(object, col = ggplot2::GeomCol$default_aes$fill, - border = ggplot2::GeomCol$default_aes$colour, \dots) +\method{autoplot}{MCdiversity}(object, col = "grey35", + border = NA, \dots) \method{summary}{MCdiversity}(object, \dots) } \arguments{ diff --git a/man/MCentropy.Rd b/man/MCentropy.Rd index d8851db..908eba7 100644 --- a/man/MCentropy.Rd +++ b/man/MCentropy.Rd @@ -13,8 +13,8 @@ \usage{ is.MCentropy(x) \method{plot}{MCentropy}(x, \dots) -\method{autoplot}{MCentropy}(object, col = ggplot2::GeomCol$default_aes$fill, - border = ggplot2::GeomCol$default_aes$colour, \dots) +\method{autoplot}{MCentropy}(object, col = "grey35", + border = NA, \dots) \method{summary}{MCentropy}(object, \dots) } \arguments{ diff --git a/man/PhyloValue.Rd b/man/PhyloValue.Rd index a3a6b5c..5c2813d 100644 --- a/man/PhyloValue.Rd +++ b/man/PhyloValue.Rd @@ -13,9 +13,9 @@ \usage{ is.PhyloValue(x) \method{autoplot}{PhyloValue}(object, xlab = expression(italic("T")), ylab = NULL, main = NULL, - col = ggplot2::GeomLine$default_aes$colour, - lty = ggplot2::GeomLine$default_aes$linetype, - lwd = ggplot2::GeomLine$default_aes$size, + col = "black", + lty = 1, + lwd = 0.5, \dots) \method{plot}{PhyloValue}(x, xlab = expression(italic("T")), ylab = NULL, main = NULL, \dots) \method{summary}{PhyloValue}(object, \dots) diff --git a/man/SpeciesDistribution.Rd b/man/SpeciesDistribution.Rd index 677d2d8..c334781 100644 --- a/man/SpeciesDistribution.Rd +++ b/man/SpeciesDistribution.Rd @@ -32,9 +32,9 @@ as.SpeciesDistribution(x, \dots) \method{as.SpeciesDistribution}{numeric}(x, \dots) \method{autoplot}{SpeciesDistribution}(object, \dots, Distribution = NULL, ylog = TRUE, main = NULL, xlab = "Rank", ylab = NULL, - pch = ggplot2::GeomPoint$default_aes$shape, - col = ggplot2::GeomPoint$default_aes$colour, - cex = ggplot2::GeomPoint$default_aes$size) + pch = 19, + col = "black", + cex = 1.5) \method{plot}{SpeciesDistribution}(x, \dots, Distribution = NULL, type = "b", log = "y", main = NULL, xlab = "Rank", ylab = NULL) is.SpeciesDistribution(x)