sbrewer's blog

• Install R and Rcmdr.
• Refer to R Commander Installation Notes for details: http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html
  • Only use binary sources
  • One a Mac, be sure to turn off "App Nap" (until "Tools" menu.)
• 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...

Please download this directory, unzip it, and work in your group to analyze the data: https://bcrc.bio.umass.edu/data_practice/data_practice_files.tar.gz

Figure 1. Microscope image of tardigrade. A diagnostic characteristic of tardigrades are the sclerotized mouthparts. "Tardigrade" flickr photo by AJC1 https://flickr.com/photos/ajc1/37884036601 shared under a Creative Commons (BY-SA) license.

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!