After sorted by one of sample annotations, is main plot sorted by mutation by that annotation

[wangzunq]

Describe the issue
So I want the oncoplot cluster by cohort, which has A, B,C and is one of sample annotations. Also, I want to still keep gene sorted by mutation frequency as well as sample sorted by mutation frequency in each cohort as well. So it looks like a waterfall for each cohort.
The question is: when I choose sortbyAnnotation(cohort) will the order per cohort is sorted by sample level mutation frequency(meaning the samples in each cohort is sorted independently according to mutation frequency)
Thank you for clarifying.

[wangzunq]

Any help is appreciated. I try to do manually to retrieve sample names that first sorted by cohort and within each to count occurrences of sample names to get the sample_order. Also, gene freq is calculated as a whole and sorted descending regardless of cohort. But it doesn’t seem like a waterfall for each cohort. Why is that?

[wangzunq]

I know gene order isn’t same if sorted by frequency for each cohort. Is there a way to make it look like a waterfall for each cohort

[PoisonAlien]

Hi,

Sorry for the delay. Could you please post an example image of what you expect and how it is being shown?

[wangzunq]

I just did and got the sample order. Default is good to go! But it takes a bit time backend sorting algorithms figuring out, I think sort by annotation and within each cluster it is sorted by gene mutation frequency. And I did manually with this sample order and compared with default it is exactly same. I just have to make sure other plots are following same order. Such as Gistic oncoplot.

[wangzunq]

Actually still different. Could you help provide the back end script that did sample order sorting? Given the df with Hugo_Symbol, tumor_bar_code, cohort. I really need the sample order is when it is automatically sorted by oncoplot. Thanks for help

[PoisonAlien]

Hi,

I still have trouble understanding the issue here. If you want the oncoplot columns to be in a specific order, try the sampleOrder argument.

[wangzunq]

Hi, What I want is the sorting algorithm for sample order that is built in oncoplot() function without using SampleOrder param. Could you help locate this ? Thanks a lot. Sent from my iPhone On Dec 17, 2024, at 03:18, Anand Mayakonda ***@***.***> wrote:  Hi, I still have trouble understanding the issue here. If you want the oncoplot columns to be in a specific order, try the sampleOrder argument. — Reply to this email directly, view it on GitHub<#1075 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BHAFOAN3QHSLXXKCPLK7NWT2F7M6JAVCNFSM6AAAAABSGDP4S2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBXG43TCMJTGE>. You are receiving this because you authored the thread.Message ID: ***@***.***> The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed. It may also contain confidential and/or privileged material. Any use of the information transmitted by persons or entities other than the intended recipient is strictly prohibited. If this email was sent to you in error and includes sensitive Dana-Farber information (for example, patient information, Social Security Numbers, credit card information), please communicate this to Dana-Farber's Compliance Hotline at www.compliancereport.org <http://www.compliancereport.org> . If the information transmitted does not contain such sensitive information, please contact the sender and properly dispose of the email. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

[PoisonAlien]

Hi,

Here is the internal function that creates the sorted onco-matrix.

[wangzunq]

Thank you! Didn’t notice it is in concomatrix script. How about the other issue for rightBarData? I want the default summarized bar plot to be plotted in left. How to get rightBarData from given MAF obj? I want it to be plotted in left instead of right. And is it possible to move % mutation rowwise on the right to left and gene names to right? Sent from my iPhone On Dec 17, 2024, at 08:44, Anand Mayakonda ***@***.***> wrote:  External Email - Use Caution Hi, Here is the internal function<https://secure-web.cisco.com/1u2RrHg4iKCRbOMC0Yxskx8-ljs7Ritb-sY1ryx9n01nOLMHCwLusTISiqpiZoLlmKNS6F8Xrgj6Od_-Yj5yEAt336R-rOuhIH1OIJ_8RwaDSyV2g4fDHCYts_qb10x_8BKqbZDGGdz_hfL2dqs8ZTyVWukapni0lSjO9KsA8FH1Yu4IFoQsSZTSeFn_-3Qk2QHO_aIvYEYOk7UNdjk2UWrAjahT_gQhCRmxRp3c9PkVOlpgSKki5yf3dfHdgmGKX55ShS_ADzLB9ENbisw9lAUwpGvyBlO9ya-tkw5lOqBqbbTpLBf914e9gowdsI3BI/https%3A%2F%2Fgithub.com%2FPoisonAlien%2Fmaftools%2Fblob%2F19f92bd56164f9aef81589f224a946cc6454dacc%2FR%2Foncomatrix.R%23L1> that creates the sorted onco-matrix. — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/1SEre0pnAfEUGT9A0lVisJSQRdHZ051anuKXT4BhHRsYMses2KnegX06v695Q5mGmwvDgzJRUjKQcOdqTZM4vgbWd9i5XrFstxOvdiy2cD70B1XMp-oNJ4VYZTn-DowzaViMpgCX0tvSDZKlviketAMcHaivyUT-uttos6BFhyt89FzmiZNtk5pUZHL0qP0PoV4VaYLn7lbP6T6ZQO6XM11pM9s6u6CFLsm7zQsam5jFFC22fsa7cl14_Et0HmDJPxNg2jcOUiMxhpVAkFvbWbEI5jHUtCtGQwKRIf6Z0bGkZ8CqK2zqm14q6iMdtGGoS/https%3A%2F%2Fgithub.com%2FPoisonAlien%2Fmaftools%2Fissues%2F1075%23issuecomment-2548499699>, or unsubscribe<https://secure-web.cisco.com/1Mw1YYy9BHcX116uRQiEGyMTNEUYbIIUA38M2yH9Ge-Mb3X4_zPA0QTnPFjOAG7poB-eBWMJ7xWYaXG3Cs-OODcxk27bo1QL0-t5IqE5CyMtyz05rTp52uYzXeicKDsI4Eyona8s6coBxkcrfyAh9W9pDN3nxFUI03EQz54fC6rJuPU3Z6jXZ7vIqRdfzExTfAV0_8IaxfDsba4hax_ha1Bjd9XnJmCpfqnk9X2GrLs_gQknYyAHdHgpjB0Kwb6auv249P_53ipXuMJ1ghg1p4L2jtJsGQn82kJusZUe2vdos5YmMgmI0cHgni12J-A4s/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FBHAFOAIRFGAAT6WTX5ZESLL2GATCZAVCNFSM6AAAAABSGDP4S2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBYGQ4TSNRZHE>. You are receiving this because you authored the thread.Message ID: ***@***.***> The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed. It may also contain confidential and/or privileged material. Any use of the information transmitted by persons or entities other than the intended recipient is strictly prohibited. If this email was sent to you in error and includes sensitive Dana-Farber information (for example, patient information, Social Security Numbers, credit card information), please communicate this to Dana-Farber's Compliance Hotline at www.compliancereport.org <http://www.compliancereport.org> . If the information transmitted does not contain such sensitive information, please contact the sender and properly dispose of the email. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.