Visualization of marker raw scores for Arabidopsis genetic map, chromosome 4:



To generate the image above run py_matrix_2D_V112_RECBIT.py script with following options:

python py_matrix_2D_V112_RECBIT.py DL_RIL_Data.may2001.out.pairs_all ath-chrom4-map.txt ath-chrom4-map.out.pymapx Dean_Lister_frame.IDs Y DL_RIL_Data.may2001.loc REC 0 0.9

(similar to py_matrix_2D_V087_RECBIT.py usage with exception of the last two additional arguments: 0 and 0.9)

upon execution several images will be generated:

ath-chrom4-map.out.pymapx.large.png - large image (full size image)
ath-chrom4-map.out.pymapx.medium.png - medium size image (1000 x 750 pixels)
ath-chrom4-map.out.pymapx.small.png - small image (200 x 150 pixels)
ath-chrom4-map.out.pymapx.2000.png - image with size 2000 x 1500 pixels (optional)
ath-chrom4-map.out.pymapx.tab - 2D matrix text file

(no difference from py_matrix_2D_V087_RECBIT.py output)

and four new files:

ath-chrom4-map.out.pymapx.xrecomb.png - image with raw scores (the same as above)
ath-chrom4-map.out.pymapx.xsparse.matrix - matrix file with linkage (1 - recombination_value) values for those pairs of markers where linkage 0.9 or better (it was last argument 0.9 of the script)
ath-chrom4-map.out.pymapx.xgraph.2500.png - really weird representation of linkage group in the form of circular graph
ath-chrom4-map.out.pymapx.xgraph.large.png - the same as above but really huge image


Note, that *.loc (DL_RIL_Data.may2001.loc) file must contain the line with RILs numbering, for example:

; 1 2 3 4 5 6 7 ....

this line is critical for proper script functionality.

you may ignore the understanding of argument 0. It was introduced for debugging purpose.

Example input files can be downloaded here


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this is a Arabidopsis genetic map of linkage group 4 in the form of circular graph:



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Printable Posters:

Download "Arabidopsis Genetic Map" poster 36 x 48 inches: ATH_GeneticMap_B1.ppt (PowerPoint format) images generated with py_matrix_2D_V087_RECBIT.py

Download "Arabidopsis Five Linkage Groups" poster 36 x 48 inches: ATH_GeneticMap_A1.ppt (PowerPoint format) images generated with py_matrix_2D_V112_RECBIT.py

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Feedback and comments are very welcome