LieberInstitute / visiumStitched

R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.
http://research.libd.org/visiumStitched/
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naming of section headings #3

Closed madhavitippani closed 3 months ago

madhavitippani commented 3 months ago

I feel like it's less confusing for readers/users to have the same section headings in both the manuscript and the docs here when following the package.

  1. change Preparing Images for Fiji in http://research.libd.org/visiumStitched/articles/visiumStitched.html to Preparing inputs to Fiji
  2. Give a section heading Stitching images with Fiji to the video section in http://research.libd.org/visiumStitched/articles/visiumStitched.html under Building a SpatialExperiment
  3. Function names not consistent in manuscript and docs, prep_fiji_coords(), prep_fiji_image() in docs and prep_image_coords() in manuscript
  4. Change the section heading from parsing outputs from Fiji to Creating group level samples or vice versa
  5. Change the section heading from Array coordinates to Defining array coordinates. Talk about the add_array_coords() function.
  6. Match the individual capture area spot colours to the colours used by Svitlana in the figure (array A - yellow, array B- green, array C - red)
  7. Maybe number the main sections in http://research.libd.org/visiumStitched/articles/visiumStitched.html, when reading through the page the text size of the main and subheadings is not always visible and thereby confusing readers if they are reading a new section or an existing section
Nick-Eagles commented 3 months ago

Thanks Maddy! I addressed everything except point 7, which I wasn't sure about. For me, both the table of contents and heading sizes delimit each section as expected