View source: R/plot_alpha_rcurve.R
plot_alpha_rcurve | R Documentation |
Calculates alpha diversity idenx at varying sampling units (sequencing depth).
plot_alpha_rcurve( x, index = "observed", subsamples = c(100, 1000, 2000, 3000, 4000, 5000), lower.conf = 0.025, upper.conf = 0.975, group = NULL, linetype.main = 1, line.opacity.main = 0.5, linetype.type = 2, line.opacity.type = 0.25, type = "CI", label.min = TRUE, label.size = 3, label.color = "grey70" )
x |
|
index |
Default:: "observed", |
subsamples |
Default: c(100,1000, 2000, 3000, 4000, 5000) |
lower.conf |
Default: 0.025. If type=CI |
upper.conf |
Default: 0.975. |
group |
Default: NULL |
linetype.main |
For ggplot line type for line by group. Default: 1 |
line.opacity.main |
For ggplot alpha to determine opacity for line by group. Default: 0.5 |
linetype.type |
For ggplot line type for line CI or SD. Default: 2 |
line.opacity.type |
For ggplot line type to determine opacity for line CI or SD. Default: 0.25 |
type |
Either CI (confidence interval) or SD (Standard deviation) Default: CI |
label.min |
TRUE or FALSE. Default: TRUE |
label.size |
Label min size |
label.color |
Label min color |
## Not run: library(microbiomeutilities) data("zackular2014") p0 <- zackular2014 # e.g. to make range of # subsamples <- seq(0, 5000, by=100)[-1] p <- plot_alpha_rcurve(p0, index="observed", lower.conf = 0.025, upper.conf = 0.975, group="DiseaseState") + scale_color_brewer(palette = "Paired") + scale_fill_brewer(palette = "Paired") print(p ) ## End(Not run)
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