sbrewer's blog

All small animals that have hard skin and six legs get bigger by getting rid of their old skin and making a new skin hard. Young of these animals just have parts for feeding and growing, but older animals need parts for having sex and making babies -- and sometimes don't need parts for feeding any more.  

Some animals grow up by changing little by little but others change themselves completely at one point. When this happens, almost all of their inside parts actually die and a whole new animal grows again from just a few tiny bits of their inside parts. When the parts die the stuff they were made out of is used by the parts still alive to grow all of the new inside parts.

Often the new animal looks very different from its young form and may have body parts like wings and sex parts that the younger form didn't have. Often these new animals don't live very long -- just long enough to have sex and then lay eggs or have babies -- and then die.

Complete this activity as background for discussing manuscript submission guidelines. Look through this list of life science journals and identify a journal that you might want to submit an article too. Google that journal to find their page of "instructions to authors" and look for their manuscript submission guideslines.  Write two or three paragraphs as an In-class Exercise that briefly summarize the kinds of specifications that the instructions to authors require.

Figure 1. Leaf Miner. Frass is visible in the gallery. "Leaf Miners" flickr photo by Smabs Sputzer (1956-2017) https://flickr.com/photos/10413717@N08/6132692653 shared under a Creative Commons (BY) license.

• Install R and Rcmdr.
• Refer to R Commander Installation Notes for details: http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html
• Import the data:
  • In Rcmdr. under “Data” menu “Import data” from “text file”
  • Set the “Field Separator” to “Commas”.
  • Navigate to the CSV file and select it.
  • Click the “Edit data set” button to open the data set in a window.
  • Make a note of all outliers (to put in the legend of the figure).
  • Click on the number of each row with an outlier, then right-click and “Delete current row”.
  • Click OK to save edited data set.
• Under “Graphs” choose “Scatterplot matrix...”
  • Select all three variables.
  • Click “Plot by groups”, select Gender, and click OK.
  • Click “Options” and select the checkbox for Least-squares line and click OK.
  • Check for outliers and repeat as necessary.
• Each student independently choose one pair of variables to report in a scatter plot
  • Choose independent and dependent variables
  • Click “Plot by groups”, select Sex, and click OK.
  • Click “Options” and select the checkbox for Least-squares line and click OK.
  • Save as PDF (use this for posters)
  • Convert to PNG (use this to post at website)
  • Post as Image: write legend that includes title, description, and reports outliers.
  • (If time available, report relevant statistics, e.g. means, linear regression, or one-way ANOVA)

GIYF and here is a book for additional assistance: https://stellmack.dl.umn.edu/sites/g/files/pua2461/f/media/_the_rcmdr_gu...

Screencasts for making multipanel scientific figures using Inkscape

Creating Figures: Part 1. Compositing
Creating Figures: Part 2. Labels and Arrows
Creating Figures: Part 3. Document Properties and Exporting

Hints

• Think ahead of time. What is your figure going to look like? Should you crop imagery ahead of time? Do you need to adjust image or exposure? (Note: Some journals don't allow digital manipulation of imagery). Do this in a bitmap editing program (e.g. GIMP or Photoshop).
• Do all your work in a folder. Put your image files in there. Save your SVG file in there. Save early and often.

Workflow

1. Import all your images: Either Link or Embed. Note things can be “above” or “below” others. Click or drag over to select. Hold the “shift” key to select multiple objects.
2. Composite your images to make your design: Lock proportions to avoid stretching. Turn “snapping” on or off. Set height and width directly to resize. Use Align and Distribute (switch to "relative to first selected").
3. Construct one label: Consider font and contrast.
4. Duplicate label to make more: Select label, duplicate object, move. Repeat as necessary.
5. Finish each label: Replace each letter as necessary. Use Align and Distribute to center. Use align and distribute to put labels at corners of each panel.
6. Create arrows: Use the Line Tool to draw a straight line segment (click, click-click). Then use Fill and Stroke tool to set the line width and add arrow head to start (or end).
7. Set the Page Size: Open Document Properties. Resize Page to Drawing. Set background to not be transparent (increase alpha channel to 255).
8. Export Finished Figure: Export PAGE. Set width to 1200pixels. Save with name “Lastname-Original.png” The resultant PNG file is your finished figure.

Note: Do not share your finished figure or include in your METHODS manuscript until your methods have been followed!