Visualizing Genes/Motifs in h5 viewer
Jen Garbarino
19 steps
2 minutes
Atlasxomics
Latch
The h5 viewer (on the welcome tab) is a great way to quickly visualize gene activity scores and motif enrichment as well as combined sets of gene/motif scores. You can find more details on how these scores are calculated from the archR documentation:\ <https://www.archrproject.com/bookdown/calculating-gene-scores-in-archr.html>\ <https://www.archrproject.com/bookdown/motif-and-feature-enrichment-with-archr.html>\ \ While this walkthrough shows the data viewed spatially, this can also be done in the UMAP view of the dataset (see main tutorial page for toggle location)
1
The h5 viewer screen can be toggled between gene activity scores and motif enrichment. To change which scores you are viewing, click the dropdown below the h5 viewer.
Single Gene Visualization
2
To visualize a gene/motif of interest, click on the plus icon in the genes of interest tab. This will say genes of interest even if visualizing motifs.
While in the H5 viewer you can tell if you are looking at motifs over genes becuase motifs each have a number at the end (ex. AR-668 motif vs AR gene). This numbering system comes from ArchR.
3
Click "Select genes..." to type in your gene/motif of interest.
4
Click on the gene in the dropdown to select that gene
5
Click "Add" to add the gene to the viewer
6
Click the dropwdown arrow to see the scale bar for this gene
7
Click the paint can to color by this gene
8
You can use the toggles on the scale bar to adjust the coloring to focus on particular portions of the data
9
For example, this allows us to more clearly visualize the variability of ACTB accessibility in this tissue
10
Click the camera icon to export plot as png. This will be downloaded to your computer.
11
Click here to change the file name. You can also choose to not include the color legend in the download (not recomended)
12
Click "Export" to save the image to your computer
For large datasets, this export can take a few minutes as any datapoints not rendered due to size are readded to the image. While you can close this message and continuing using the viewer, you cannot export another image until the first one is completed.
Multiple Gene Scores
13
When clicking on the plus to add genes, you can select multiple genes of interest.
14
All the genes added will be available on the left side of the viewer
15
click the paint can to change to another gene/motif or add to a gene/motif set
16
Click "Create gene coloring set" to add to the currently visualized gene/motif
17
The combined score is now instead displayed on the h5 viewer.
18
Once added, you can click the paint can again to remove from gene coloring set or to instead only color by this gene.
19
Click the three dots next to gene of interest to clear all selected genes as needed.
Visualizing Genes/Motifs in h5 viewer
Jen Garbarino
19 steps
2 minutes
Atlasxomics
Latch
The h5 viewer (on the welcome tab) is a great way to quickly visualize gene activity scores and motif enrichment as well as combined sets of gene/motif scores. You can find more details on how these scores are calculated from the archR documentation:\ <https://www.archrproject.com/bookdown/calculating-gene-scores-in-archr.html>\ <https://www.archrproject.com/bookdown/motif-and-feature-enrichment-with-archr.html>\ \ While this walkthrough shows the data viewed spatially, this can also be done in the UMAP view of the dataset (see main tutorial page for toggle location)
1
The h5 viewer screen can be toggled between gene activity scores and motif enrichment. To change which scores you are viewing, click the dropdown below the h5 viewer.
Single Gene Visualization
2
To visualize a gene/motif of interest, click on the plus icon in the genes of interest tab. This will say genes of interest even if visualizing motifs.
While in the H5 viewer you can tell if you are looking at motifs over genes becuase motifs each have a number at the end (ex. AR-668 motif vs AR gene). This numbering system comes from ArchR.
3
Click "Select genes..." to type in your gene/motif of interest.
4
Click on the gene in the dropdown to select that gene
5
Click "Add" to add the gene to the viewer
6
Click the dropwdown arrow to see the scale bar for this gene
7
Click the paint can to color by this gene
8
You can use the toggles on the scale bar to adjust the coloring to focus on particular portions of the data
9
For example, this allows us to more clearly visualize the variability of ACTB accessibility in this tissue
10
Click the camera icon to export plot as png. This will be downloaded to your computer.
11
Click here to change the file name. You can also choose to not include the color legend in the download (not recomended)
12
Click "Export" to save the image to your computer
For large datasets, this export can take a few minutes as any datapoints not rendered due to size are readded to the image. While you can close this message and continuing using the viewer, you cannot export another image until the first one is completed.
Multiple Gene Scores
13
When clicking on the plus to add genes, you can select multiple genes of interest.
14
All the genes added will be available on the left side of the viewer
15
click the paint can to change to another gene/motif or add to a gene/motif set
16
Click "Create gene coloring set" to add to the currently visualized gene/motif
17
The combined score is now instead displayed on the h5 viewer.
18
Once added, you can click the paint can again to remove from gene coloring set or to instead only color by this gene.
19
Click the three dots next to gene of interest to clear all selected genes as needed.
