plot_landscape {microbiome} | R Documentation |
Wrapper for visualizing sample similarity landscape ie. sample density in various 2D projections.
plot_landscape(x, method = "PCoA", distance = "bray", transformation = "identity", col = NULL, main = NULL, x.ticks = 10, rounding = 0, add.points = TRUE, adjust = 1, size = 1, legend = FALSE, shading = TRUE)
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.
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")