This guide shows the files to plot idiograms of measured karyotypes and optionally marks.

1 Load package

visit gitlab for installation instructions https://gitlab.com/ferroao/idiogramFISH

2 Get your chromosome size data

Initially you have to open your chromosome data as a data.frame.

loading saved data:

Initially, if you use RStudio, use menu “Session”, “Set working directory” for choosing your desired folder or:

setwd("~/folder/subfolder")

Open your chromosome data data.frame importing it from a .csv (read.csv) or .xls file (readxl).

mydfChrSize<-read.csv("somefile.csv")

For fixing column names use:

colnames(mydfChrSize)<-c("OTU", "chrName","shortArmSize","longArmSize")

3 Get marks general data

This data.frame is optional for ver. > 1.0.0

Open or make your mark data as a data.frame. This data.frame has the marks present in all karyotypes without position info. If style column is not present it will be filled with square during plotting.

markName markColor style
5S red dots
45S green square
DAPI blue square
CMA yellow square

For fixing column names use:

colnames(mydfMarkColor)<-c("markName", "markColor","style") 

4 Get marks positions data

Open or write your mark positions as a data.frame. This data.frame has the marks present in all karyotypes with position info.

OTU chrName markName markArm markSize markDistCen
Species one 1 5S p 0.5 0.5
Species one 1 45S q 1.0 0.5
Species one X 45S p 1.0 1.0
Species one 3 DAPI q 1.0 1.0

For fixing column names use something like:

colnames(mydfMarkColor)<-c("OTU", "chrName","markName","markArm","markSize","markDistCen") 

5 Special data.frame for centromeric marks’ data

Open or make your mark data as a data.frame. This data.frame has the centromeric marks present in all karyotypes. Only for centromereSize >0.

OTU chrName markName
Species one 1 DAPI
Species one X CMA

6 Plotting

You can plot without marks (use only 1st data.frame), but we will use all 4 data.frames created. By default the function will calculate indices and morphological categories (Levan et al., 1964; Guerra, 1986; Romero-Zarco, 1986; Watanabe et al., 1999). Use parameters of the function to modify that. See ?plotIdiograms

After v. 1.1.0, vertices when centromereSize=0 are rounded:

For ver. > 1.0.0 there is no need to add dfMarkColor and you can also use the parameter mycolors (optional too), to establish marks’ colors. Colors are assigned depending on the order of marks, i.e.:

unique(c(dfOfMarks$markName,dfOfCenMarks$markName) )

charVectorCol <- c("tomato3","darkolivegreen4","dfsd","blue","green")

plotIdiograms(dfChrSize=dfOfChrSize, 
              dfMarkPos=dfOfMarks, 
              chrColor = "gray",
              cenColor = "gray",
              dfCenMarks=dfOfCenMarks,
              
              mycolors = charVectorCol,
              
              dotRoundCorr=2, chrWidth=2.5, chrSpacing = 2.5,
              karSpacing=1.6, 
              indexIdTextSize=1, 
              markLabelSize=1, 
              rulerPos=-1.9, ruler.tck=-0.02, rulerNumberPos=.5, rulerNumberSize=1
)

7 Example with several species (OTUs)

To illustrate this, we will load some data.frames from the package

Chromosome sizes

OTU chrName shortArmSize longArmSize
Species 1 1 1.5 2.0
Species 1 2 2.0 2.5
Species 1 3 1.0 1.5
Species 2 1 3.0 4.0
Species 2 2 4.0 5.0
Species 2 3 2.0 3.0
Species 2 X 1.0 2.0
Species 2 4 3.0 4.0
Species 3 1 3.2 4.0
Species 3 2 4.5 5.0
Species 3 3 2.0 3.0
Species 3 4 1.5 2.0
Species 3 5 4.8 6.0
Species 3 6 6.1 7.0
Species 4 1 1.5 2.0
Species 4 2 2.0 2.5
Species 4 3 1.0 1.5
Species 5 1 3.0 4.0
Species 5 2 4.0 5.0
Species 5 3 2.0 3.0
Species 5 X 1.0 2.0
Species 5 4 3.0 4.0
Species 6 1 3.2 4.0
Species 6 2 4.5 5.0
Species 6 3 2.0 3.0
Species 6 4 1.5 2.0
Species 6 5 4.8 6.0
Species 6 6 6.1 7.0

Mark characteristics, optional for ver. > 1.0.0, does not require OTU

markName markColor style
5S red dots
45S green square
DAPI blue square
CMA yellow square

Mark position

OTU chrName markName markArm markDistCen markSize
Species 1 1 5S p 0.5 1
Species 1 1 45S q 0.5 1
Species 1 2 45S p 1.0 1
Species 1 3 DAPI q 1.0 1
Species 3 3 5S p 1.0 1
Species 3 3 DAPI q 1.0 1
Species 3 4 45S p 2.0 1
Species 3 4 DAPI q 2.0 1
Species 3 5 CMA q 2.0 1
Species 3 6 5S q 0.5 1

Centromeric Marks only

OTU chrName markName
Species 2 1 DAPI
Species 2 4 CMA

References

Guerra M. 1986. Reviewing the chromosome nomenclature of Levan et al. Brazilian Journal of Genetics, 9(4): 741–743

Levan A, Fredga K, Sandberg AA. 1964. Nomenclature for centromeric position on chromosomes Hereditas, 52(2): 201–220. https://doi.org/10.1111/j.1601-5223.1964.tb01953.x

Romero-Zarco C. 1986. A new method for estimating karyotype asymmetry Taxon, 35(3): 526–530. https://onlinelibrary.wiley.com/doi/abs/10.2307/1221906

Watanabe K, Yahara T, Denda T, Kosuge K. 1999. Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information Journal of Plant Research, 145–161. http://link.springer.com/article/10.1007/PL00013869