How to Color Each Atom (TAD) According to Its Gene Expression Level
Dear ChimeraX Users Help,
I want to color each atom, which is a TAD, according to its genes’ expression value.
My code writes a Chimera marker file because it has RGB variables (shown below, the lower the gene expression, the lighter the shade of green). However, ChimeraX shows the entire model in the same color. How should I color each atom (TAD) according to its gene expression level? [image: image.png]
Thank you.
Best regards, Zichen “Cardiff” Jiang
Hi Cardiff,
The ChimeraX marker files use red, green, blue values in the range 0-1, not 0-255. So your color components greater than 1 are probably all just being treated as 1.
Tom
On May 15, 2021, at 11:00 AM, Cardiff Jiang z8jiang@ucsd.edu wrote:
Dear ChimeraX Users Help,
I want to color each atom, which is a TAD, according to its genes’ expression value.
My code writes a Chimera marker file because it has RGB variables (shown below, the lower the gene expression, the lighter the shade of green). However, ChimeraX shows the entire model in the same color. How should I color each atom (TAD) according to its gene expression level?
Thank you.
Best regards, Zichen “Cardiff” Jiang -- Best regards, Zichen “Cardiff” Jiang _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Tom,
Got it. Thank you!
Best regards, Zichen “Cardiff” Jiang
On Sat, May 15, 2021 at 11:07 AM Tom Goddard goddard@sonic.net wrote:
Hi Cardiff,
The ChimeraX marker files use red, green, blue values in the range 0-1, not 0-255. So your color components greater than 1 are probably all just being treated as 1.
Tom
On May 15, 2021, at 11:00 AM, Cardiff Jiang z8jiang@ucsd.edu wrote:
Dear ChimeraX Users Help,
I want to color each atom, which is a TAD, according to its genes’ expression value.
My code writes a Chimera marker file because it has RGB variables (shown below, the lower the gene expression, the lighter the shade of green). However, ChimeraX shows the entire model in the same color. How should I color each atom (TAD) according to its gene expression level? [image: image.png]
Thank you.
Best regards, Zichen “Cardiff” Jiang -- Best regards, Zichen “Cardiff” Jiang
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!Mih3wA!Xv0_QscH1AyB5c22fvwb3z__bBuw7wzWhnp_kqL1OK6GPScI_CdeoZ_2PVN5kpme$
--
Best regards, Zichen “Cardiff” Jiang
participants (2)
-
Cardiff Jiang -
Tom Goddard