get_Muller_df: Create a data frame from which to create a Muller plot

Description Usage Arguments Value Author(s) See Also Examples

View source: R/MullerPlot.R

Description

Create a data frame from which to create a Muller plot

Usage

1
2
get_Muller_df(edges, pop_df, cutoff = 0, start_positions = 0.5,
  threshold = NA, add_zeroes = NA, smooth_start_points = NA)

Arguments

edges

Dataframe comprising an adjacency matrix, or tree of class "phylo"

pop_df

Dataframe with column names "Identity", "Population", and either "Generation" or "Time"

cutoff

Numeric cutoff; genotypes that never become more abundant than this value are omitted

start_positions

Numeric value between 0 and 1 that determines the times at which genotypes are assumed to have arisen (see examples)

threshold

Depcrecated (use cutoff instead, but note that "threshold" omitted genotypes that never become more abundant than *twice* its value)

add_zeroes

Deprecated (now always TRUE)

smooth_start_points

Deprecated (now always TRUE)

Value

A dataframe that can be used as input in Muller_plot and Muller_pop_plot.

Author(s)

Rob Noble, robjohnnoble@gmail.com

See Also

Muller_plot Muller_pop_plot

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
# by default, all genotypes are included, 
# but one can choose to omit genotypes with max frequency < cutoff:
Muller_df <- get_Muller_df(example_edges, example_pop_df, cutoff = 0.01)

# the genotype names can be arbitrary character strings instead of numbers:
example_edges_char <- example_edges
example_edges_char$Identity <- paste0("foo", example_edges_char$Identity, "bar")
example_edges_char$Parent <- paste0("foo", example_edges_char$Parent, "bar")
example_pop_df_char <- example_pop_df
example_pop_df_char$Identity <- paste0("foo", example_pop_df_char$Identity, "bar")
Muller_df <- get_Muller_df(example_edges_char, example_pop_df_char, cutoff = 0.01)

# the genotype names can also be factors (which is the default for strings in imported data):
example_edges_char$Identity <- as.factor(example_edges_char$Identity)
example_edges_char$Parent <- as.factor(example_edges_char$Parent)
example_pop_df_char$Identity <- as.factor(example_pop_df_char$Identity)
Muller_df <- get_Muller_df(example_edges_char, example_pop_df_char, cutoff = 0.01)

# to see the effect of changing start_positions, compare these two plots:
edges1 <- data.frame(Parent = c(1,2,1), Identity = 2:4)
pop1 <- data.frame(Time = rep(1:4, each = 4), 
                    Identity = rep(1:4, times = 4),
                    Population = c(1, 0, 0, 0, 
                                   2, 2, 0, 0, 
                                   4, 8, 4, 0, 
                                   8, 32, 32, 16))
df0 <- get_Muller_df(edges1, pop1, start_positions = 0)
df1 <- get_Muller_df(edges1, pop1, start_positions = 1)
Muller_plot(df0)
Muller_plot(df1)

ggmuller documentation built on Sept. 5, 2019, 9:04 a.m.