diff --git a/.Rproj.user/A7880BF4/sources/prop/3C94AC20 b/.Rproj.user/A7880BF4/sources/prop/3C94AC20 index 7a8d269..5036cfc 100644 --- a/.Rproj.user/A7880BF4/sources/prop/3C94AC20 +++ b/.Rproj.user/A7880BF4/sources/prop/3C94AC20 @@ -1,6 +1,6 @@ { "source_window_id": "", "Source": "Source", - "cursorPosition": "4,73", + "cursorPosition": "1,17", "scrollLine": "0" } \ No newline at end of file diff --git a/_bookdown.yml b/_bookdown.yml index 4b13ca3..49fe121 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,5 +1,5 @@ book_filename: "bookdown-thesis.Rmd" -output_dir: "book" +output_dir: "docs" delete_merged_file: true always_allow_html: yes new_session: true # required for kableExtra to play nicely with bookdown \ No newline at end of file diff --git a/book/01_intro.md b/docs/01_intro.md similarity index 100% rename from book/01_intro.md rename to docs/01_intro.md diff --git a/book/02_chapter2.md b/docs/02_chapter2.md similarity index 100% rename from book/02_chapter2.md rename to docs/02_chapter2.md diff --git a/book/03_chapter3.md b/docs/03_chapter3.md similarity index 100% rename from book/03_chapter3.md rename to docs/03_chapter3.md diff --git a/book/04_chapter4.md b/docs/04_chapter4.md similarity index 99% rename from book/04_chapter4.md rename to docs/04_chapter4.md index 592a875..1548b09 100644 --- a/book/04_chapter4.md +++ b/docs/04_chapter4.md @@ -39,8 +39,8 @@ Several functions in the easyXpress package require specific naming conventions ```{=html} -
- +
+ ``` The naming of "Metadata_Plate" and "Metadata_Well" are essential to the *setflags()*, *viewPlate()*, *viewWell()*, and *viewDose()* functions. Additionally, "Image_fileName_RawBF" and "Image_PathName_RawBF" are necessary for the proper function of *viewDose()*. diff --git a/book/05_discussion.md b/docs/05_discussion.md similarity index 100% rename from book/05_discussion.md rename to docs/05_discussion.md diff --git a/book/06_references.md b/docs/06_references.md similarity index 100% rename from book/06_references.md rename to docs/06_references.md diff --git a/book/07_appendix.md b/docs/07_appendix.md similarity index 100% rename from book/07_appendix.md rename to docs/07_appendix.md diff --git a/book/404.html b/docs/404.html similarity index 100% rename from book/404.html rename to docs/404.html diff --git a/book/a-role-for-cuticle-stretch-in-developmental-growth-control.html b/docs/a-role-for-cuticle-stretch-in-developmental-growth-control.html similarity index 100% rename from book/a-role-for-cuticle-stretch-in-developmental-growth-control.html rename to docs/a-role-for-cuticle-stretch-in-developmental-growth-control.html diff --git a/book/a.-growth-dynamics-of-c.-elegans-cuticle-mutants.html b/docs/a.-growth-dynamics-of-c.-elegans-cuticle-mutants.html similarity index 100% rename from book/a.-growth-dynamics-of-c.-elegans-cuticle-mutants.html rename to docs/a.-growth-dynamics-of-c.-elegans-cuticle-mutants.html diff --git a/book/appendix.html b/docs/appendix.html similarity index 100% rename from book/appendix.html rename to docs/appendix.html diff --git a/book/b.-food-allocation-during-c.-elegans-growth.html b/docs/b.-food-allocation-during-c.-elegans-growth.html similarity index 100% rename from book/b.-food-allocation-during-c.-elegans-growth.html rename to docs/b.-food-allocation-during-c.-elegans-growth.html diff --git a/book/dedication.html b/docs/dedication.html similarity index 100% rename from book/dedication.html rename to docs/dedication.html diff --git a/book/discussion-2.html b/docs/discussion-2.html similarity index 100% rename from book/discussion-2.html rename to docs/discussion-2.html diff --git a/book/easyxpress-an-r-package-to-analyze-and-visualize-c.-elegans-microscopy-data-generated-using-cellprofiler.html b/docs/easyxpress-an-r-package-to-analyze-and-visualize-c.-elegans-microscopy-data-generated-using-cellprofiler.html similarity index 99% rename from book/easyxpress-an-r-package-to-analyze-and-visualize-c.-elegans-microscopy-data-generated-using-cellprofiler.html rename to docs/easyxpress-an-r-package-to-analyze-and-visualize-c.-elegans-microscopy-data-generated-using-cellprofiler.html index d3c2ee6..b7c23a7 100644 --- a/book/easyxpress-an-r-package-to-analyze-and-visualize-c.-elegans-microscopy-data-generated-using-cellprofiler.html +++ b/docs/easyxpress-an-r-package-to-analyze-and-visualize-c.-elegans-microscopy-data-generated-using-cellprofiler.html @@ -275,8 +275,8 @@

4.4.3 Paraquat dose response

4.4.4 Naming conventions

Several functions in the easyXpress package require specific naming conventions to work properly. For full details regarding essential file naming and directory structure see the package repository (https://github.com/AndersenLab/easyXpress). Importantly, when using the Metadata module in CellProfiler to extract information describing your images, specific column names are suggested.

-
- +
+

The naming of “Metadata_Plate” and “Metadata_Well” are essential to the setflags(), viewPlate(), viewWell(), and viewDose() functions. Additionally, “Image_fileName_RawBF” and “Image_PathName_RawBF” are necessary for the proper function of viewDose().

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