humann2_barplot sample labels not displayed

[utritala]

Hello,

I am trying to use humann2_barplot but the sample labels are not displayed. 

My input file and the output image is attached with this email. Here is my command:

humann2_barplot -i all_samples_pathabundances_humann2_relab_stratified_for_plotting.pcl -f 1CMET2-PWY --focal-metadatum Infant --output all_samples_pathabundances_humann2_relab_stratified_humann2_barplot2.png

Any help you could provide will be great. 

Many thanks. 

[Eric Franzosa]

It looks like I didn't include labeling the samples as an option since the tool was benchmarked on very large datasets (where labels would be inconvenient). I'll note it as something to add for a future release. The best (very sub-optimal) solution for now would be to include the sample labels as a metadata row.

Thanks,

Eric

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[Urmi]

Thanks Eric.  I have already put in samples (shown as "Infant") as metadata row. For example:

#FEATURE        Q117    Q142    Q175    Q189    Q19     Q216    Q219    Q26     Q83     Q87     Q89

#Infant Q117    Q142    Q175    Q189    Q19     Q216    Q219    Q26     Q83     Q87     Q89

UNINTEGRATED|g__Bifidobacterium.s__Bifidobacterium_breve        0       0       0       0       0       0       0.250506        0.324136        0       0.698905        0

But the results still stay the same. Please correct me if I am wrong. 

On Tuesday, August 6, 2019 at 7:58:51 PM UTC+1, Eric Franzosa wrote:

It looks like I didn't include labeling the samples as an option since the tool was benchmarked on very large datasets (where labels would be inconvenient). I'll note it as something to add for a future release. The best (very sub-optimal) solution for now would be to include the sample labels as a metadata row.

Thanks,

Eric

On Tue, Aug 6, 2019 at 11:49 AM utritala <urm...@gmail.com> wrote:

Hello,

I am trying to use humann2_barplot but the sample labels are not displayed. 

My input file and the output image is attached with this email. Here is my command:

humann2_barplot -i all_samples_pathabundances_humann2_relab_stratified_for_plotting.pcl -f 1CMET2-PWY --focal-metadatum Infant --output all_samples_pathabundances_humann2_relab_stratified_humann2_barplot2.png

Any help you could provide will be great. 

Many thanks. 

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[John G]

Hi Eric,

Is there any way you can send a hack to accomplish this task, even if privately? I'd also like to get the samples on the x-axis and ideally I'd be able to do so in the next week. I've made my way through the script that accomplishes this task, but there is a lot going on that my non-coding brain has difficulty wrapping around. My guess is that for someone more familiar with scripting it wouldn't be a huge change?

John

On Tuesday, August 6, 2019 at 11:58:51 AM UTC-7, Eric Franzosa wrote:

It looks like I didn't include labeling the samples as an option since the tool was benchmarked on very large datasets (where labels would be inconvenient). I'll note it as something to add for a future release. The best (very sub-optimal) solution for now would be to include the sample labels as a metadata row.

Thanks,

Eric

On Tue, Aug 6, 2019 at 11:49 AM utritala <urm...@gmail.com> wrote:

Hello,

I am trying to use humann2_barplot but the sample labels are not displayed. 

My input file and the output image is attached with this email. Here is my command:

humann2_barplot -i all_samples_pathabundances_humann2_relab_stratified_for_plotting.pcl -f 1CMET2-PWY --focal-metadatum Infant --output all_samples_pathabundances_humann2_relab_stratified_humann2_barplot2.png

Any help you could provide will be great. 

Many thanks. 

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[Eric Franzosa]

You might be hitting an issue because of the #s in the feature names. The following command worked for me (note the use of \ for escape):

humann2_barplot -i test.pcl -l \#Infant -m \#Infant -f 1CMET2-PWY -o test.png

(I renamed your input to test.pcl.) This produced the attached graphic.

Thanks,

Eric

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[John G]

Hi Eric,

I was able to get this approach to work, but I have 12 samples and it appears the color map is rather small as there are colors overlapping (see attached). I don't see the options for colormap, but was hoping to find a scale that would encompass a greater range. I'll dig into matplotlib color palettes a bit as I assume it is in there (??), but if you could get back to me that would be great. Also, I can't get all 20 in the legend without going off the bottom. I've messed around with the various spacing options, but none seem to suffice. So if you have any thoughts on that topic, as well, that would be great. Finally, is there a reason the leftmost bar is half the size of all the others? That doesn't seem to be the case with your image.

humann2_barplot  --input input.tsv --focal-feature ARGSYN-PWY --output ARGSYN-PWY-out -l \#sampleID -m \#sampleID -x -z

I'm using humann2-0.11.2

John

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