Convert independent_filtering_plots.Rnw to independent_filtering_plots.Rmd#6
Convert independent_filtering_plots.Rnw to independent_filtering_plots.Rmd#6villafup wants to merge 5 commits intoBioconductor:develfrom
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@Bioconductor/sweave2rmd I kept the last two graphs separated. It didn't seem to make sense to collapse them into the same row since the 2nd happens under a different numbered section. |
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Flagging to remove the extra carriage return here
| The output is shown in the right panel of Fig. \@ref(fig:filter-volcano). | ||
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| ```{r filter-volcano, fig.cap = "Left panel: plot produced by the filter_volcano function. Right panel: graph of the `kappa_t` function."} |
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(You may have already been working with this) but it looks like this syntax is not shown in the original vignette PDF. Please add echo=FALSE to the chunk header to hide the code
| ```{r sessionInfo, echo=FALSE} | ||
| sessionInfo() | ||
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Do we know how to add a header that isn't reflected in the table of contents? Ideally, it would be nice to add a "References" header here to match the original vignette but I don't want it to show up in the TOC. This is something I was playing w/ in another vignette I converted and I have not come up with a clean answer. Do you have any ideas @villafup ?
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I added the reference as a side note under the "Introduction" section. We can add the reference at the bottom like in the original vignette, but I think we'd need to add another file to the vignette folder. It's definitely doable.
| for the $p$-values. For these data, over a reasonable range of FDR | ||
| cutoffs, increased filtering corresponds to increased rejections. | ||
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| ```{r rejection-plot, fig.cap = "Plot produced by the `rejection_plot function`"} |
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In the vignette PDF, I see that "Figure 2" is in bold black font and the caption is black font whereas this caption has bold blue font as the caption text. Is this an easy edit? Not sure whether it would be a headache to match the original vignette PDF or not.
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We might be able to accomplish this with the MiKTeX package, but do we want to have another library?
| main="Benjamini & Hochberg adjustment") | ||
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| The plot is shown in Fig. \@ref(fig:rejection-plot). |
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I know we've had a difficult time as a group figuring out how to format these figures so that they're side-by-side. I checked in with Jen during our last Sweave meeting and because the different formatting doesn't significantly change reader's understanding, it sounds like we can keep them in current format, one on top of the other
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I changed the wording of some of the comments and captions. We should double-check to make sure they're right.
Also, l moved the lines "The output is shown in Fig ..." above each graph to be consistent with the first graph. This line was below all the graphs except Figure 1. Let me know you would this editorial change changed back.
jwokaty
changed the title
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