You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hello Folks,
I realised this issue might be similar to #69 (comment), but I think there are unsolved questions in the closed issues 69.
I found that the .cafe file genereted by CAFE5 is different from the .cafe file generated by CAFE4 (4.2.1), like @Xacfran has mentioned in issues 69, the Viterby-P-values column in CAFE4' result is not presented by CAFE5, which might casue wrong outputs of CAFE_fig (all nodes show +0/-0 expanded and contracted gene family, when not using --count_all_expansions option in CAFE_fig). The result of my data, looks like this:
I used command: python3 CAFE_fig.py Base_report.cafe --dump test/, and some warning messages have jumped out:
"Parsing CAFE report... done!
Writing test/summary.pdf
qt.qpa.xcb: failed to initialize XRandr
qt.qpa.xcb: X server does not support XInput 2
qt.qpa.xcb: XKeyboard extension not present on the X server"
, and generated the above figure.
If I added --count_all_expansions in my command, the tree nodes will show the numbers of all expanded and contracted gene families, but still a condensed tree shape, like this:
I know there is a visualization tools designed specifically for CAFE5 called CAFE_plotter, but it could only show numbers of all expanded and contracted gene families on the tree (this was confirmed by its author).
As in my case, I am only interested in presenting the number of gene families which have gone through change with statistical significance, instead of showing the big number of all expanded/contracted gene families, is there a easy way by using CAFE5, like omitting count_all_expansions in CAFE_fig?
(By the way, I know how to caculate the number of significantly expanded/contracted gene families of tree nodes using awk and grep command from CAFE5 result files, for example *_family_results.txt and *_change.tab).
The text was updated successfully, but these errors were encountered:
Hello Folks,
I realised this issue might be similar to #69 (comment), but I think there are unsolved questions in the closed issues 69.
I found that the .cafe file genereted by CAFE5 is different from the .cafe file generated by CAFE4 (4.2.1), like @Xacfran has mentioned in issues 69, the Viterby-P-values column in CAFE4' result is not presented by CAFE5, which might casue wrong outputs of CAFE_fig (all nodes show +0/-0 expanded and contracted gene family, when not using --count_all_expansions option in CAFE_fig). The result of my data, looks like this:
I used command: python3 CAFE_fig.py Base_report.cafe --dump test/, and some warning messages have jumped out:
"Parsing CAFE report... done!
Writing test/summary.pdf
qt.qpa.xcb: failed to initialize XRandr
qt.qpa.xcb: X server does not support XInput 2
qt.qpa.xcb: XKeyboard extension not present on the X server"
, and generated the above figure.
If I added --count_all_expansions in my command, the tree nodes will show the numbers of all expanded and contracted gene families, but still a condensed tree shape, like this:
I know there is a visualization tools designed specifically for CAFE5 called CAFE_plotter, but it could only show numbers of all expanded and contracted gene families on the tree (this was confirmed by its author).
As in my case, I am only interested in presenting the number of gene families which have gone through change with statistical significance, instead of showing the big number of all expanded/contracted gene families, is there a easy way by using CAFE5, like omitting count_all_expansions in CAFE_fig?
(By the way, I know how to caculate the number of significantly expanded/contracted gene families of tree nodes using awk and grep command from CAFE5 result files, for example *_family_results.txt and *_change.tab).
The text was updated successfully, but these errors were encountered: