tidypopgen (version 0.4.3)

autoplot_q_matrix: Autoplots for q_matrix objects

Description

This autoplot will automatically rearrange individuals according to their id and any grouping variables if an associated 'data' gen_tibble is provided. To avoid any automatic re-sorting of individuals, set arrange_by_group and arrange_by_indiv to FALSE.

Usage

# S3 method for q_matrix
autoplot(
  object,
  data = NULL,
  annotate_group = TRUE,
  arrange_by_group = TRUE,
  arrange_by_indiv = TRUE,
  reorder_within_groups = FALSE,
  ...
)

Value

a barplot of individuals, coloured by ancestry proportion

Arguments

object

A Q matrix object (as returned by q_matrix()).

data

An associated tibble (e.g. a gen_tibble), with the individuals in the same order as the data used to generate the Q matrix

annotate_group

Boolean determining whether to annotate the plot with the group information

arrange_by_group

Boolean determining whether to arrange the individuals by group. If the grouping variable in the gen_tibble or the metadata of the gt_admixt object is a factor, the data will be ordered by the levels of the factor; else it will be ordered alphabetically.

arrange_by_indiv

Boolean determining whether to arrange the individuals by their individual id (if arrange_by_group is TRUE, they will be arranged by group first and then by individual id, i.e. within each group). If id in the get_tibble or the metadata of the gt_admix object is a factor, it will be ordered by the levels of the factor; else it will be ordered alphabetically.

reorder_within_groups

Boolean determining whether to reorder the individuals within each group based on their ancestry proportion (note that this is not advised if you are making multiple plots, as you would get a different order for each plot!). If TRUE, annotate_group must also be TRUE.

...

not currently used.

Examples

# Read example gt_admix obejct
admix_obj <-
  readRDS(system.file("extdata", "anolis", "anole_adm_k3.rds",
    package = "tidypopgen"
  ))

# Extract a Q matrix
q_mat_k3 <- get_q_matrix(admix_obj, k = 3, run = 1)

# Basic autoplot
autoplot(q_mat_k3, annotate_group = FALSE, arrange_by_group = FALSE)

# To arrange individuals by group and by Q proportion
autoplot(q_mat_k3,
  annotate_group = TRUE, arrange_by_group = TRUE,
  arrange_by_indiv = TRUE, reorder_within_groups = TRUE
)