Description Usage Arguments Details Value Examples
View source: R/plot_landscape.R
Wrapper for visualizing sample similarity landscape ie. sample density in various 2D projections.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
x |
|
method |
Ordination method, see phyloseq::plot_ordination; or "PCA", or "t-SNE" (from the Rtsne package) |
distance |
Ordination distance, see phyloseq::plot_ordination; for method = "PCA", only euclidean distance is implemented now. |
transformation |
Transformation applied on the input object x |
col |
Variable name to highlight samples (points) with colors |
main |
title text |
x.ticks |
Number of ticks on the X axis |
rounding |
Rounding for X axis tick values |
add.points |
Plot the data points as well |
adjust |
Kernel width adjustment |
size |
point size |
legend |
plot legend TRUE/FALSE |
shading |
Add shading in the background. |
For consistent results, set random seet (set.seed) before function call. Note that the distance and transformation arguments may have a drastic effect on the outputs.
A ggplot
plot object.
1 2 3 4 5 6 7 8 9 10 11 | data(dietswap)
# PCoA
p <- plot_landscape(transform(dietswap, "compositional"),
distance = "bray", method = "PCoA")
p <- plot_landscape(dietswap, method = "t-SNE", distance = "bray",
transformation = "compositional")
# PCA
p <- plot_landscape(dietswap, method = "PCA", transformation = "clr")
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