Labeled Volcano Plot from DE

[JasonWReeves]

Inputs

• [x] Left / Right labels
• [x] Gene List to Show or max # of genes to label by Significance/FC
• [x] FDR / P-value Threshold & FC Threshold
• [x] Color Options
• [x] Font size & family
• [x] Plot Size (height / width)

Requirements

• [x] User uploads a results table from a statistical test as a CSV
• [x] Show enrichment direction
• [x] Color by enrichment direction
• [x] Prefer actual P-value on y-axis (0.1, 0.01, 0.001, 1e-4, etc)
• [x] Point size is static
• [x] Show lines for FC & P-value/FDR thresholds
• [x] Label Axes for FC directionality
• [x] Label points with gene list or # of genes provided by user above
• [x] Dotted line for FDR cutoff with option to not show this line

Stretch

• [ ] Vignette with instructions on how to choose the FDR --> biostats
• [x] Add names or coloring by tags

[JasonWReeves]

Anticipated steps for data processing:

1. Load data from de_table.csv/xlsx
2. Bin data & identify genes to label
3. Graph data
4. Save graph

[NicoleEO]

Notes from Maddy: I couldn't figure out how to put the pvalue on the y axis if you want to add that but it was a nice to have rather than required. the label size isn't a user option but it does change based on number of labels. so I guess pay attention to those and see if they are too small or too big. the VOLCANO PLOT file from DSPDA must be changed to a \t delimited file and the header can be removed though it doesn't need to be.

[NicoleEO]

@dnadave is there someone in biostats who would like to add to @maddygriz vignette about how to choose your FDR cutoff? This is a stretch goal, but I believe CX thought it would help the customers.

[dnadave]

Lei Yang should be able to do this.

On Mon, Nov 30, 2020 at 4:14 PM Nicole Ortogero notifications@github.com wrote:

@dnadave https://github.com/dnadave is there someone in biostats who would like to add to @maddygriz https://github.com/maddygriz vignette about how to choose your FDR cutoff. This is a stretch goal, but I believe CX thought it would help the customers.

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[NicoleEO]

@yangleicq can you add a blurb in the vignette instructing customers on how to go about picking your FDR. Here's the link to the vignette: https://github.com/Nanostring-Biostats/DSPPlugins/tree/volcano-plugin/DSPPlugVolcanoPlot