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jiwoongbio / FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
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Interpretation of FMAP pathway plot #9

Closed ayan05 closed 6 years ago

ayan05 commented 6 years ago

Hi, I am working on a dataset consisting of normal and crohn's disease patients sample. After mapping KO genes to pathways I am getting a plot of pathways, but how to determine those differentially abundant pathways are from which sample?

jiwoongbio commented 6 years ago

Hi, I made a modification of FMAP_plot.pl code to show up/down proportions as red/blue colors on the plot bars. Please try the new FMAP_plot.pl Thanks for your feedback!

On Wed, Mar 28, 2018 at 5:49 AM, ayan05 notifications@github.com wrote:

Hi, I am working on a dataset consisting of normal and crohn's disease patients sample. After mapping KO genes to pathways I am getting a plot of pathways, but how to determine those differentially abundant pathways are from which sample?

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ayan05 commented 6 years ago

Thank you! Best, Ayan

sturne29 commented 5 years ago

Just to clarify: if you have a "control" and a "treatment" group, would the red indicate pathways that are more abundant in the treatment as compared to the control? I'm having a bit of trouble parsing the graph output.

jiwoongbio commented 5 years ago

@sturne29 Yes, you are right.

TakacsBertalan commented 3 years ago

Hi! I have a question about how to interpret the pathway plot. If I understand correctly, the bar is red if the indicated pathway is more abundant in my group than in the control, and blue if the pathway is more abundant in the control. My problem is that the plot created from my data shows multi-colored bars for several pathways and I am having a hard time interpreting this. Can it be a statistical error because of the small sample size (3 samples per group)? pathway_plot.pdf

Thanks in advance!

EDIT: Okay, I think I got it. The bars show the whole pathway which consists of several genes. So it's possible for some members of the pathway to seem more abundant, while some are less abundant as in the control.