IBRtools (version 0.1.3)

ibr_chart: IBR Radarchart

Description

Plots the IBR standardized values for the enzymes to be compared with one another.

Usage

ibr_chart(
  df,
  axistype,
  pcol,
  pfcol,
  plwd,
  plty,
  cglcol,
  cglty,
  axislabcol,
  cglwd,
  caxislabels,
  seg,
  legend = NULL,
  ...
)

Value

Returns a radarchart with the standardized values of biomarkers

Arguments

df

A data.frame that resulted from the function ibr_std

axistype

The type of axes, specified by any of 0:5. 0 means no axis label. 1 means center axis label only. 2 means around-the-chart label only. 3 means both center and around-the-chart (peripheral) labels. 4 is *.** format of 1, 5 is *.** format of 3. Default is 0.

pcol

A vector of color codes for plot data: Default 1:8, which are repeatedly used.

pfcol

A vector of color codes for filling polygons: Default NA, which is repeatedly usd.

plwd

A vector of line widths for plot data: Default 1, which is repeatedly used.

plty

A vector of line types for plot data: Default 1:6, which are repeatedly used.

cglcol

Line color for radar grids: Default "navy"

cglty

Line type for radar grids: Default 3, which means dotted line.

axislabcol

Color of axis label and numbers: Default "blue"

cglwd

Line width for radar grids: Default 1, which means thinnest line.

caxislabels

Character vector for center axis labels, overwriting values specified in axistype option. If NULL, the values specified by axistype option are used. Default is NULL.

seg

The number of segments for each axis (default 4).

legend

Default is NULL, when any other value is given the legend will not appear and you can manually create your own using the legend() function right after building your radarchart

...

Miscellaneous arguments to be given for plot.default().

Tips

If you have any problems with the axis labels, you can do it manually by changing two params in the function: seg and caxislabel. The caxislabel param has to be a sequence, such as: caxislabels = seq(-1,1.9,0.34), each number is: seq(minvalue, maxvalue, breakvalue)

The seg param can be any number starting from 3, you can change it with: seg = 6.

If you still can't solve the problem, try rounding your standardized values with the function round()

References

Beliaeff, B., & Burgeot, T. (2002). Integrated biomarker response: A useful tool for ecological risk assessment. Environmental Toxicology and Chemistry, 21(6), 1316–1322.

Devin, S., Burgeot, T., Giambérini, L., Minguez, L., & Pain-Devin, S. (2014). The integrated biomarker response revisited: Optimization to avoid misuse. Environmental Science and Pollution Research, 21(4), 2448–2454. https://doi.org/10.1007/s11356-013-2169-9

Minato Nakazawa (2022). fmsb: Functions for Medical Statistics Book with some Demographic Data. R package version 0.7.0. https://CRAN.R-project.org/package=fmsb

Examples

data(enzact)

ibr_std(enzact) -> enzact_chart

ibr_chart(enzact_chart, legend = FALSE)

colorvector<- c(rgb(1,0.4,0.8,0.7), rgb(0,0.6,0.6,0.7) , rgb(0.4,0.4,0.6,0.7), rgb(0,0.4,0.4,0.7))

legend(x=1.2, y=-0.3, enzact_chart$group, bty = "n", pch=20, col=colorvector, cex=0.9, pt.cex=2)