Labeled Volcano Plot - vignette and parameters

[rvitancol]

Add the following sections in the vignette

• [x] Loading into the DSP-DA - Rename Running the plugin section to Loading into the DSP-DA. Add the section on how to run plugins in DSP-DA at the beginning of this section. (Refer to Dim Reduction Plugin)

• [x] Setting User Parameters - be more specific, what values can the parameters take

• [x] Example Parameter Set-up - change the Interpretation of Results Section to Example Parameter Set-up

• [x] Interpretation of Results - maybe we can skip this for now. I will confirm with Prajan if he needs this for volcano plot.

• [x] R script - change the Target Name to Target name or better to make it case insensitive.

[stegemang]

Is the docx up to date? Do users need to remove certain rows from the volcano plot xlsx export before saving as a tab delimited file? I am triggering an error about incorrect rows removed when I try to test this.

[maddygriz]

@stegemang I think something got updated in the column names from the volcano plot.xlsx file. The script looks currently looks for "Target Name" case sensitive but in the new output it is "Target name". That is getting changed in the script soon but the quick fix is to capitalize the N in the output file.

[maddygriz]

I have updated the script to make the search for Target Name case insensitive. https://github.com/Nanostring-Biostats/DSPPlugins/commit/5303703feec53095f48cad78f7bccbacc995b9ce

[maddygriz]

Vignette has been updated to look more like the Dim Reduction vignette.

[rvitancol]

closing this issue. Volcano plot is merged in master branch.