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Update plot-methods.R #1779

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Update plot-methods.R #1779

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23 changes: 21 additions & 2 deletions R/plot-methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -666,7 +666,7 @@ plot_net <- function(physeq, distance="bray", type="samples", maxdist = 0.7,
#' plot_richness(GlobalPatterns, x="SampleType", measures=c("Chao1", "ACE", "InvSimpson"), nrow=3)
#' plot_richness(GlobalPatterns, x="SampleType", measures=c("Chao1", "ACE", "InvSimpson"), nrow=3, sortby = "Chao1")
plot_richness = function(physeq, x="samples", color=NULL, shape=NULL, title=NULL,
scales="free_y", nrow=1, shsi=NULL, measures=NULL, sortby=NULL){
scales="free_y", nrow=1, shsi=NULL, measures=NULL, sortby=NULL, boxplot=FALSE){
# Calculate the relevant alpha-diversity measures
erDF = estimate_richness(physeq, split=TRUE, measures=measures)
# Measures may have been renamed in `erDF`. Replace it with the name from erDF
Expand Down Expand Up @@ -772,6 +772,25 @@ plot_richness = function(physeq, x="samples", color=NULL, shape=NULL, title=NULL
if( !is.null(title) ){
p <- p + ggtitle(title)
}
if (boxplot == TRUE) {
# Make the ggplot.
p = ggplot(mdf, richness_map) + geom_boxplot(na.rm=TRUE)
# Add error bars if mdf$se is not all NA
if( any(!is.na(mdf[, "se"])) ){
p = p + geom_errorbar(aes(ymax=value + se, ymin=value - se), width=0.1)
}
# Rotate horizontal axis labels, and adjust
p = p + theme(axis.text.x=element_text(angle=-90, vjust=0.5, hjust=0))
# Add y-label
p = p + ylab('Alpha Diversity Measure')
# Facet wrap using user-options
p = p + facet_wrap(~variable, nrow=nrow, scales=scales)
# Optionally add a title to the plot
if( !is.null(title) ){
p <- p + ggtitle(title)
}
}

return(p)
}
################################################################################
Expand Down Expand Up @@ -2840,4 +2859,4 @@ plot_clusgap = function(clusgap, title="Gap Statistic results"){
p = p + ggtitle(title)
return(p)
}
################################################################################
################################################################################