This guide shows the files to plot idiograms of karyotypes of holocentrics 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.

or loading saved data:

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

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

For fixing column names use:

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 with color and style, 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:

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 markPos markSize chrRegion
Species one 4 B NA NA w
Species one 3 DAPI 2.0 0.5
Species one 1 45S 2.0 0.5
Species one 2 DAPI 2.0 0.5
Species one X CMA 2.0 0.5
Species one X 5S 0.5 0.5
Species one X 5S 0.5 0.5

For fixing column names use something like:

5 Plotting

function plotIdiogramsHolo deprecated after ver. > 1.5.1

You can plot without marks (passing only 1st data.frame), but we will use all 4 data.frames created:

It is not mandatory to use dfMarkColor and you can also use the parameter mycolors (optional too), to establish marks’ colors. When using mycolors, colors are assigned depending on the order of marks, i.e.:

6 Example with several species (OTUs)

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

  • Chromosome sizes
OTU chrName chrSize
species one 1 5.1
species one 2 5.0
species one 3 4.9
species one 4 5.2
species two 1 3.0
species two 2 4.0
species two 3 2.0
species two 4 5.0
species three 1 1.5
species three 2 2.0
species three 3 6.0
species three 4 8.0
  • Mark characteristics, does not require OTU
  • d.f optional for ver. > 1.0.0
markName markColor style
5S red dots
45S green square
DAPI blue square
CMA yellow square
  • Mark position
OTU chrName markName markPos markSize
species two 3 5S 1.0 0.5
species two 3 DAPI 2.0 0.5
species two 1 45S 2.0 0.5
species two 2 DAPI 2.0 0.5
species two 4 CMA 2.0 0.5
species two 4 5S 0.5 0.5

7 Using bases instead of micrometers

Create some data in millions of bases:

8 GISH of holocentric chromosomes

You need the data.frame of chr. sizes, and a d.f. of marks

Chr. sizes:

parentalAndHybHoloChrSize
OTU chrName chrSize
Parental 1 7 4
Parental 1 4 2
Parental 1 5 6
Parental 1 6 7
Parental 2 1 4
Parental 2 2 5
Parental 2 3 3
Allopolyploid 7 4
Allopolyploid 2 5
Allopolyploid 3 3
Allopolyploid 4 2
Allopolyploid 5 6
Allopolyploid 6 7

Marks’ positions data

dfAlloParentMarksHolo
OTU chrName markName chrRegion
1 Allopolyploid 7 Parental 1 w
4 Allopolyploid 2 Parental 2 w
5 Allopolyploid 3 Parental 2 w
6 Allopolyploid 4 Parental 1 w
7 Allopolyploid 5 Parental 1 w
8 Allopolyploid 6 Parental 1 w
9 Parental 1 6 Parental 1 w
10 Parental 1 5 Parental 1 w
11 Parental 1 7 Parental 1 w
12 Parental 1 4 Parental 1 w
13 Parental 2 2 Parental 2 w
14 Parental 2 1 Parental 2 w
15 Parental 2 3 Parental 2 w