umap: A umap function
This is a flexible umap function that can be run on a standard data frame. It is a wrapper for umap/ggplot2 code and can be customised with different colours and font sizes and more.
umap(mydata, labels = FALSE, printres = FALSE, seed = FALSE,
axistextsize = 18, legendtextsize = 18, dotsize = 5,
textlabelsize = 4, legendtitle = "Group", controlscale = FALSE,
scale = 1, low = "grey", high = "red", colvec = c("skyblue",
"gold", "violet", "darkorchid", "slateblue", "forestgreen", "violetred",
"orange", "midnightblue", "grey31", "black"), printheight = 20,
printwidth = 22, text = FALSE)mydata |
Data frame or matrix: if dataframe/matrix should have samples as columns and rows as features |
labels |
Character vector: if we want to just label with gender for example |
printres |
Logical flag: whether to print the UMAP into current directory |
seed |
Numerical value: optionally set the seed |
axistextsize |
Numerical value: axis text size |
legendtextsize |
Numerical value: legend text size |
dotsize |
Numerical value: dot size |
textlabelsize |
Numerical value: text inside plot label size |
legendtitle |
Character vector: text legend title |
controlscale |
Logical flag: whether to control the colour scale |
scale |
Numerical value: 1=spectral palette, 2=manual low and high palette, 3=categorical labels |
low |
Character vector: continuous scale low colour |
high |
Character vector: continuous scale high colour |
colvec |
Character vector: a series of colours in vector for categorical labels, e.g. c("sky blue", "gold") |
printheight |
Numerical value: png height |
printwidth |
Numerical value: png width |
text |
Character vector: if we wanted to label the samples with text IDs to look for outliers |
A umap plot object
UMAP <- umap(mydata)
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