reading tmap files

[broadinstitute]

reading tmap files

[joshua-gould]

Transport map files were corrupted. Fixed by regenerating.

[geoffschieb]

Hi Zinaida, We have just released WOT 1.0, along with a tutorial: https://broadinstitute.github.io/wot/tutorial/ I'm sending this to anyone who has expressed interest recently. Best, Geoff Be

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On Fri, Apr 5, 2019 at 6:20 PM Zinaida Good ***@***.***> wrote: Hello Joshua, I'm a postdoc working on engineered T cells at Stanford university and hope to use WOT. I've generated maps from the attached data matrix and days file using the following command: wot optimal_transport --matrix matrix.txt --cell_days days.txt --local_pca 0 --out tmaps However, I can't seem to solve the error in calculating the trajectory generated by this command (screenshot attached): wot trajectory --tmap tmaps --cell_set naive.gmt --day 10 --out wot_trajectory.txt I'm also attaching the gmt file used for this command that contains the following information. Tip1 naive CD8_HA_D0_213 CD8_HA_D0_298 CD8_HA_D0_362 CD8_HA_D0_413 CD8_HA_D0_561 CD8_HA_D0_722 CD8_HA_D0_798 CD8_HA_D0_829 CD8_HA_D0_893 CD8_HA_D0_896 The issue appears to be with getting information out of the loom files. Could ou please help? Thanks in advance, Zina [image: wot-error] <https://user-images.githubusercontent.com/8445659/55659364-31a3e600-57b6-11e9-952d-6778adedd738.png> matrix.txt <https://github.com/broadinstitute/wot/files/3049827/matrix.txt> days.txt <https://github.com/broadinstitute/wot/files/3049828/days.txt> naive.txt <https://github.com/broadinstitute/wot/files/3049830/naive.txt> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#46>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJIoYpZop38GB29Buus3oKHM0Yv7a1Uzks5vd8xJgaJpZM4cf0ZH> .

[zinagood]

Nice! Thanks so much!! Zina

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Sent from my iPhone

On May 11, 2019, at 5:17 AM, geoffschieb ***@***.***> wrote: Hi Zinaida, We have just released WOT 1.0, along with a tutorial: https://broadinstitute.github.io/wot/tutorial/ I'm sending this to anyone who has expressed interest recently. Best, Geoff Be On Fri, Apr 5, 2019 at 6:20 PM Zinaida Good ***@***.***> wrote: > Hello Joshua, > > I'm a postdoc working on engineered T cells at Stanford university and > hope to use WOT. > > I've generated maps from the attached data matrix and days file using the > following command: > wot optimal_transport --matrix matrix.txt --cell_days days.txt --local_pca > 0 --out tmaps > > However, I can't seem to solve the error in calculating the trajectory > generated by this command (screenshot attached): > wot trajectory --tmap tmaps --cell_set naive.gmt --day 10 --out > wot_trajectory.txt > > I'm also attaching the gmt file used for this command that contains the > following information. > Tip1 naive CD8_HA_D0_213 CD8_HA_D0_298 CD8_HA_D0_362 CD8_HA_D0_413 > CD8_HA_D0_561 CD8_HA_D0_722 CD8_HA_D0_798 CD8_HA_D0_829 CD8_HA_D0_893 > CD8_HA_D0_896 > > The issue appears to be with getting information out of the loom files. > Could ou please help? > > Thanks in advance, > Zina > > [image: wot-error] > <https://user-images.githubusercontent.com/8445659/55659364-31a3e600-57b6-11e9-952d-6778adedd738.png> > matrix.txt > <https://github.com/broadinstitute/wot/files/3049827/matrix.txt> > days.txt <https://github.com/broadinstitute/wot/files/3049828/days.txt> > naive.txt <https://github.com/broadinstitute/wot/files/3049830/naive.txt> > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#46>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/AJIoYpZop38GB29Buus3oKHM0Yv7a1Uzks5vd8xJgaJpZM4cf0ZH> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.