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I was revisiting this figure and in going through it in more detail, I found that the heatmap colors were not consistent with the copy number values and some values were not being printed.
Head of CN dataframe for 3770, where column 4 is copy number
Pag3770_1 1445001 1495000 6.186963177
Pag3770_1 3070001 3125000 2.815778549
Pag3770_1 4385001 4475000 2.578674358
Pag3770_1 6745001 6860000 10.48400049
Pag3770_1 9375001 9560000 6.840217837
Here is the figure.
Chromosome 1 of 3770 is missing the CNV at 3 Mb and 1 CNV on chromsome 7 has been labelled "red", when it should have been "blue".
Is there a way to control the colors so that all copy numbers <2 get labelled red and those >2 labelled blue? I thought this is what was happening, but it seems not.
I am happy to share the copy number file, if it helps.
As always, your help is much appreciated.
Diya
The text was updated successfully, but these errors were encountered:
Hi Bernat,
I was revisiting this figure and in going through it in more detail, I found that the heatmap colors were not consistent with the copy number values and some values were not being printed.
Here is the code.
Head of CN dataframe for 3770, where column 4 is copy number
Pag3770_1 1445001 1495000 6.186963177
Pag3770_1 3070001 3125000 2.815778549
Pag3770_1 4385001 4475000 2.578674358
Pag3770_1 6745001 6860000 10.48400049
Pag3770_1 9375001 9560000 6.840217837
Here is the figure.
Chromosome 1 of 3770 is missing the CNV at 3 Mb and 1 CNV on chromsome 7 has been labelled "red", when it should have been "blue".
Is there a way to control the colors so that all copy numbers <2 get labelled red and those >2 labelled blue? I thought this is what was happening, but it seems not.
I am happy to share the copy number file, if it helps.
As always, your help is much appreciated.
Diya
The text was updated successfully, but these errors were encountered: