vasarely: vasarely chart

In imbs-hl/vasarely:

Description

vasarely produces a so called vasarely chart. E.g. for some (genetic) input data expected and observed relative frequencies of allele combinations can be calculated and plotted. For all possible combinations the expected relative frequency is described by a geom_raster plot. Each cell of the plot has a color which depends on the value of the expected relative frequcency. The real relative frequency is described by a dot in the corresponding cell which also has a color that depends on the calculated relative frequency. The chart and its colors for the two relative frequencies help to check how expected and observed relative frequencies differ from each other.

Usage

vasarely(data, color = grey.colors(256, start = 1, end = 0),
  name_xaxis = "allele 2", name_yaxis = "allele 1", lower_color_value = 0,
  upper_color_value = 1)

Arguments

data	The input data to create the chart, e.g. genetic snp data. The input data must have exactly to columns.
color	The optional colors which should be used for the chart, e.g. blues9. Color must be a character vector with at least two colors. If color is NULL grey values will be taken.
name_xaxis	The optional title for the x-axis of the plot. Otherwise the x-axis is called "allele 2" as a genetic input is expected.
name_yaxis	The optional title for the y-axis of the plot. Otherwise the y-axis is called "allele 1" as a genetic input is expected.
lower_color_value	The lower limit for spreading the color over the relative frequencies values. It must be a number between 0 and 1.
upper_color_value	The upper limit for spreading the color over the relative frequencies values. It must be a number between 0 and 1.

Value

returns a list of the calculated relative frequencies, the number of observations, the vasarely chart and a list of the p-value and statistic of a chi-squared test.

Examples

# create data
a1 <- c(rep("A", each = 25), rep("B", each = 75))
a2 <- c(rep("A", each = 50), rep("B", each = 50))
data <- data.frame(a1, a2)

# use function
vasarely(data = data, color = c("yellow", "red"),
name_xaxis = "a1", name_yaxis = "a2")

imbs-hl/vasarely documentation built on May 7, 2019, 8:17 a.m.