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Question: data orders in plotcorrelation
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gravatar for sophialovechan
2.2 years ago by
sophialovechan • 10
sophialovechan • 10 wrote:

Hi, I am using galaxy-deeptools to analyze my data. But when I used plot correlation to visualize the correlation of my different cells, I don't know how to arrange the order of my samples. How can I do that rather than automatically generating the order? Thanks.
galaxy • 543 views
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modified 2.2 years ago by Devon Ryan • 1.9k • written 2.2 years ago by sophialovechan • 10
2
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

The order of the output in plotCorrelation is the order of the input bigWig files in multiBigwigSummary or the BAM files in multiBamSummary. This in turn ends up being the order in your history (from top (highest history item number) to bottom (lowest history item number)). This is...not exactly ideal or even remotely apparent, but the only way to do things with the kind of "multi-select box" that we're using. An alternative would be for us to change how the BAM/bigWig files are selected such that you can only select one at a time (it's mimic the regions in computeMatrix).

Please feel free to follow (and comment on!) deepTools issue #428, which I've opened so we can discuss how to better handle this, since I totally agree that how it's currently done isn't exactly great.
ADD COMMENT • link modified 2.2 years ago • written 2.2 years ago by Devon Ryan • 1.9k

Update: I'll make a change for the 2.4 release that will allow you to manually set the order of the samples. The expected release date for this is November 1st, so this will presumably be available on the deeptools-galaxy server a week or two after that (there's a bit of a delay between the command line and Galaxy release).

ADD REPLY • link written 2.2 years ago by Devon Ryan • 1.9k

Hi Devon,

Thank you for the updating the tools. However, I still have the issue about the arrange the order of my samples. The plotCorrelation tool doesn't follow what I set the order of the samples. The output doesn't really follow the order on the history either. The plotCorrelation version Galaxy Version 2.5.0.0 and multiBigwigSummary is also Galaxy Version 2.5.0.0. Could you please kindly advise me how I could solve the issue? Many thanks

ADD REPLY • link written 10 weeks ago by liuc • 0
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