Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

heatmap is empty with se entropy normalization #4

Closed
ecwheele opened this issue Aug 14, 2017 · 4 comments
Closed

heatmap is empty with se entropy normalization #4

ecwheele opened this issue Aug 14, 2017 · 4 comments

Comments

@ecwheele
Copy link
Collaborator

Command:

/home/bay001/projects/codebase/rbp-maps/maps/plot_density.py --ip /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW34_SRSF2_n212_diff_IP.merged.r2.bam --input /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW_diff_input_master_R1.adapterTrim.round2.rmRep.rmDup.sorted.r2.bam --annotations /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_unchanged_SE.txt --annotation_type rmats rmats rmats --output /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/rbpmaps_encode/se_entropy/EW34_SRSF2_n212_diff_IP.svg --event se --normalization_level 2 --chrom_sizes /projects/ps-yeolab/genomes/hg19/hg19.chrom.sizes

output looks like this:

screen shot 2017-08-14 at 12 27 46 pm
@ecwheele
Copy link
Collaborator Author

ecwheele commented Aug 14, 2017 •
edited
Loading

Also this warning message is thrown:

/home/ecwheele/anaconda2/envs/rbp-maps/lib/python2.7/site-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "```

@byee4
Copy link
Member

byee4 commented Aug 14, 2017 via email

@ecwheele
Copy link
Collaborator Author 

-rw-r--r-- 1 ecwheele yeo-group  5876194 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.txt.input.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group  6022791 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.txt.ip.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group  5035985 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.txt.input.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group 10974706 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.txt.ip.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group  9013912 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.txt.input.raw_density.txt
-rw-r--r-- 1 ecwheele yeo-group 13665546 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.normed_matrix.txt
-rw-r--r-- 1 ecwheele yeo-group 12787827 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.normed_matrix.txt
-rw-r--r-- 1 ecwheele yeo-group 20715093 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.normed_matrix.txt
-rw-r--r-- 1 ecwheele yeo-group    25011 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.means.txt
-rw-r--r-- 1 ecwheele yeo-group    25056 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.means.txt
-rw-r--r-- 1 ecwheele yeo-group    25057 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.means.txt
-rw-r--r-- 1 ecwheele yeo-group    25048 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.sems.txt
-rw-r--r-- 1 ecwheele yeo-group    25032 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.sems.txt
-rw-r--r-- 1 ecwheele yeo-group    25064 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.sems.txt
-rw-r--r-- 1 ecwheele yeo-group        0 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_included_SE.zscores.txt
-rw-r--r-- 1 ecwheele yeo-group        0 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_skipped_SE.zscores.txt
-rw-r--r-- 1 ecwheele yeo-group        0 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.wt_vs_mut_diff_unchanged_SE.zscores.txt
-rw-r--r-- 1 ecwheele yeo-group   350430 Aug 14 13:57 EW42_SRSF2_C1-8_diff_IP.svg```

@byee4
Copy link
Member

byee4 commented Aug 15, 2017

Please use the --bgnum and --to_test commands to specify which annotations are used as backgrounds:

/home/bay001/projects/codebase/rbp-maps/maps/plot_density.py --ip /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW34_SRSF2_n212_diff_IP.merged.r2.bam --input /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/pipeline_output_v1/EW_diff_input_master_R1.adapterTrim.round2.rmRep.rmDup.sorted.r2.bam --annotations /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_unchanged_SE.txt --annotation_type rmats rmats rmats --output EW34_SRSF2_n212_diff_IP.svg --event se --normalization_level 2 --chrom_sizes /projects/ps-yeolab/genomes/hg19/hg19.chrom.sizes --bgnum 2 --to_test /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_included_SE.txt /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/rmats/wt_vs_mut_diff_skipped_SE.txt

@byee4 byee4 closed this as completed Aug 15, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@byee4 @ecwheele