batch model: how to set copy number range about igv

[jrobinso]

Batch commands are described here https://igv.org/doc/desktop/#UserGuide/tools/batch/ See "preference"

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On Wed, Jul 10, 2024 at 7:09 AM TheOne ***@***.***> wrote: Hi Dear IGV team, I am trying to generate screenshot based on seg file in batch model. I would like to set negative range from -0.05 to -0.5, positive range from 0.05 to 0.5, value between -0.05 to 0.05 to be white. I had tried the following two ways: echo "CN_FREQ.AMP_THRESHOLD 0.05" >>igv.pref echo "CN_FREQ.DEL_THRESHOLD -0.05" >>igv.pref xvfb-run /path/to/igv.sh --preference itv.pref or echo "preference CN_FREQ.AMP_THRESHOLD 0.05" >>igv_script.bat echo "preference CN_FREQ.DEL_THRESHOLD -0.05" >>igv_script.bat xvfb-run /path/to/igv.sh -b igv_script.bat However, both of them are not work. Can you tell me how to set the value in batch model? Thanks for any help in advance! — Reply to this email directly, view it on GitHub <#1534>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HHG25SVVPFVTND2F43ZLU6CXAVCNFSM6AAAAABKU77CLWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYDAOBYGYZDQNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lamz138138]

Hi @jrobinso ! Thanks for your quick response. I generated above two ways after reading the describe below, but they are not work, so I open this issue. Is it because I did not write it correct? Besides, I do not know how to write colorScale.

##Segmented Copy Number Track Defaults
CN_FREQ.AMP_THRESHOLD CN freq amplification threshold float 0.1
CN_FREQ.DEL_THRESHOLD CN freq deletion threshold float -0.1
NO_DATA.COLOR No data color 216,216,216
NO_CALL.COLOR No call color 150,150,150
COLOR_LEGENDS Color Legends colorScale

[jrobinso]

I'm not sure what you are showing me. Could you post the actual batch script you are using?

[lamz138138]

Here are my files and command:

cat igv.pref
IGV.Bounds=0, 0, 2560, 1440

cat igv_script.bat
new
geome hg38
expand Refseq%20Genes
preference CN_FREQ.AMP_THRESHOLD 0.05
preference CN_FREQ.DEL_THRESHOLD -0.05
load input_cnv_ratio.seg
snapshotDirectory /path/to/igv_screenshot
goto chr3 35483850 35794496
region chr3 35639173 35794496
snapshot temp.png
exit

xvfb-run -d -s "-screen 0 2560X1440X24" /path/to/igv/install/2.16.0/igv.sh -b igv_script.bat --preferences igv.pref

I am not sure whether "CN_FREQ.AMP_THRESHOLD 0.05" and "CN_FREQ.DEL_THRESHOLD -0.05" will set value [-0.05, 0.5] to white. I also want to know how can I set the maximum value to 0.5 and the minimum value to -0.5?
Current, for example, I have a segment value is -0.09, it will be white after running above command, but I would like to make it light blue.

[jrobinso]

The easiest way to discover preferences syntax is to configure what you want in the UI, then look at the "prefs.properties" file in your igv folder. You can edit heatmap legends visually from the "View > Color Legends" menu. Here's the result of a rather random edit

COLOR_SCALE_COPY_NUMBER=ContinuousColorScale;-0.5;-2.5;0.5;2.5;102,255,51;255,255,255;0,204,204

The thresholds you are setting only impact the frequency track that appears above the heatmap, they have no impact on the color scale

[lamz138138]

This is really helpful. I solve the problem. Thank you very much!