Comut plot for 10 genes #11
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I am going to be out of town, with limited access to my laptop. Could you please make a comut plot with these 10 genes, a plot without and 1 with the numbers mentioned next to each of the genes (except RB1)? Thank you! |
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All of these genes but |
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They are from the 4datasetnonsilent file, gene column. Please make sure you count each gene:patient combination only once.
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On Apr 6, 2017, at 11:03 AM, Victor Lin ***@***.***> wrote:
All of these genes but RB1 and P53 (which is labeled as TP53) are not in the file data/SigGenes_001.txt nor data/SigGenes_005.txt. Is there another file that contains all the genes?
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Previously the genes were sorted based on p-value from I am using this as an input file: |
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The order can be the frequency of genes? Or the order from the number I sent you, next to the genes, with P53 and RB1 at the top. Sorry I am traveling, might respond late.
Thanks,
Varsha
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On Apr 6, 2017, at 1:32 PM, Victor Lin ***@***.***> wrote:
Previously the genes were sorted based on p-value from data/SigGenes_*.txt. Should it just use a pre-defined order so that p-value will not be needed?
I am using this as an input file:
$ cat genes.txt
P53
RB1
NONO 0.520
RNF8 0.604
FAM75A6 0.607
ZNF385D 0.631
POP7 0.669
MYADM 0.695
ADCY10 0.803
NGLY1 0.830
HIST2H2AB 0.925
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Agree with Varsha,
could either based on frequency or the value (from highest 0.925 to the
lowest 0.520).
…On 4/6/17 1:59 PM, varsh1090 wrote:
The order can be the frequency of genes? Or the order from the number
I sent you, next to the genes, with P53 and RB1 at the top. Sorry I am
traveling, might respond late.
Thanks,
Varsha
Sent from my iPhone
> On Apr 6, 2017, at 1:32 PM, Victor Lin ***@***.***> wrote:
>
> Previously the genes were sorted based on p-value from
data/SigGenes_*.txt. Should it just use a pre-defined order so that
p-value will not be needed?
>
> I am using this as an input file:
>
> $ cat genes.txt
> P53
> RB1
> NONO 0.520
> RNF8 0.604
> FAM75A6 0.607
> ZNF385D 0.631
> POP7 0.669
> MYADM 0.695
> ADCY10 0.803
> NGLY1 0.830
> HIST2H2AB 0.925
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
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-------------------------------------------------------------
Lei Zhou (B.Med. Ph.D.)
Associate Professor
Department of Molecular Genetics and Microbiology
College of Medicine
Member, UF Health Cancer Center & UF Genetics Institute
University of Florida
PO Box 103633
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List of genes with scores: data/gene-lists/genes.txt `--p_value` and `--gene_list_file` are disjointly two primary filters and sort methods, with `--num_genes` being an additional cutoff. #11
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The plot is generated. Here are the relevant files: Base directory:
Also, @varsh1090 you mentioned to count each gene:patient combination only once. They are being counted once, however currently it is taking the very last mutation type encountered in the dataset file, regardless of the previous ones. For example, if this was part of the file: The only mutation type information stored for ( |
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Thanks Victor, I'll take a look when I get a chance. I think for this figure, we might not need to mention the mutation type info.
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On Apr 6, 2017, at 3:54 PM, Victor Lin ***@***.***> wrote:
The plot is generated. Here are the relevant files:
Base directory: /ufrc/zhou/share/projects/bioinformatics/SCLC/sclc-scripts/
Gene list file: data/gene-lists/genes.txt
Comutation plot: results/SCLC_comut_plot_040617.pdf
Sample IDs: results/SampleIDs_040617.txt
Also, @varsh1090 you mentioned to count each gene:patient combination only once. They are being counted once, however currently it is taking the very last mutation type encountered in the dataset file, regardless of the previous ones.
For example, if this was part of the file:
TP53 Sample1 4
RB1 Sample1 3
TP53 Sample1 6
The only mutation type information stored for (TP53, Sample1) would be 6. Is this the desired behavior?
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Sounds good. The mutation type concern also applies to all the previous comutation plots that were generated by this script. |
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Can we also make the plot without the mutation types colored? For this figure and also the figure with the top 8 most significant genes? Thanks |
* pass arguments directly to functions * add argument to generate color map (default no color map) * make mutation_type_map a global definition * remove unnecessary color generating functions * filter by num_genes was not working properly, — fixed
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Generated the plots. The files are in You can see the commands I used to generate the plot in the file |
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Thanks! Can we also make 1 for p<0.001 genes? The top 8 in the list. |
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Here is a list of all the most recent plots and sample IDs:
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Thanks Victor! |
Hi Victor, I need some help with making a comut plot for these 10 genes -
RB1
NONO 0.520
RNF8 0.604
FAM75A6 0.607
ZNF385D 0.631
POP7 0.669
MYADM 0.695
ADCY10 0.803
NGLY1 0.830
HIST2H2AB 0.925
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