archaic_plot: STRUCTURE plot and logo plot representation of the...

In kkdey/aRchaic: Exploration, Visualization and Clustering of DNA damage patterns

Description

Takes the clustering model fit from archaic_fit as an input and plots the clusters using as EDLogo plots (Dey et al 2018) and the proportional mixing of the clusters for each sample using a STRUCTURE plot (Pritchard et al 2000, Dey2017) representation.

Usage

archaic_plot(
  model,
  topic_cols = c("red", "blue", "darkgoldenrod1", "cyan", "firebrick", "green",
    "hotpink", "burlywood", "yellow", "darkgray", "deepskyblue", "darkkhaki", "brown4",
    "darkorchid", "magenta", "yellow", "azure1", "azure4"),
  background = "modern",
  structure.control = list(),
  logo.control = list(),
  output_dir = NULL
)

Arguments

model	Fitted model from archaic_fit.
topic_cols	A vector of color assignment to the clusters/topics used for cluster representation in the STRUCTURE (Rosenberg2002) representation in archaic_plot().
background	if equals "modern", as in the default, compares enrichment of mismatch features against a modern background - else uses a background with equal probability of all mismatch features.
structure.control	The control or tuning parameters for the STRUCTURE plot representation structure.pdf output of archaic_plot (Dey2017)
logo.control	The control or tuning parameters for the EDLogo plots representation logo_clus_*.pdf output of archaic_plot (Dey2018)
output_dir	The path/directory where to save the output plots

Value

Returns a structure.pdf and as many logo plots of the form logo_clus_k.pdf for each cluster k, in the output path provided output_dir.

References

Rosenberg2002. Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A. and Feldman, M.W., 2002. Genetic structure of human populations. science, 298(5602), pp.2381-2385.

Dey2017. Dey, K.K., Hsiao, C.J. and Stephens, M., 2017. Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS genetics, 13(3), p.e1006599.

Dey2018. Dey, K.K., Xie, D. and Stephens, M., 2017. A new sequence logo plot to highlight enrichment and depletion. bioRxiv, p.226597.

Pritchard2002. Pritchard, J.K., Stephens, M. and Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2), pp.945-959.

kkdey/aRchaic documentation built on Jan. 17, 2021, 5:33 p.m.