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Looking at a Leaf

Submitted by ifernandez on Tue, 07/09/2019 - 15:13

Not exactly sure what type of leaf it is. Its length is greater than its width.
The top side has a distinct white/yellow line that resembles some sort of outline,
however this white line outline does not appear on the bottom side of the leaf.
On a side note, the leaf's edge is not a smooth rounded one, but instead it's rather jagged.
From the stem the leaf begins to widen its shape until about two thumb lengths away,
and after that it beings to narrow until it reaches its full length at the tip of the
leaf a little over another thumb length away. In addition, the leaf is not very sturdy in structure,
instead it's flimsy and weak and feels like any applied force could rip it apart.
The measured length is 14.40 cm and the measured width is roughly 4.0 cm.
The stem which continues throughout the leaf has small white hairs on the bottom of the leaf.
There is a small cut on the left side of the leaf about 6.0 cm from the start of the stem.
There is also a small circle, which I believe is a tiny hole in the center of the leaf about 0.60 cm from the tip.
The right side of the leaf has 23 tips while the left side of the leaf only has 22 tips.
Also after letting the leaf's stem sit in water for a small period of time (almost 30 minutes?) the leaf is not as
flimsy as it was when received.

Leaf Observations

Submitted by srbuckley on Tue, 07/09/2019 - 15:12

Specimen: One green leaf approximately 6.5 inches long. Has a elliptical shape with pointy ends. Has a serrated appearance on the edges. The width of where the stem was attached to the mother plant is about .25 inches across.
Interesting Features: There is a lighter green ribbon like structure across one vertical half of the leaf, on the right side. It almost appears as if someone drizzled the leaf with a lighter green paint. There appears to be two separate "tracks" of this lighter green. It looks to me like an insect was eating parts of the leaf and this is the track left by that. The tracks are minuscule in width. I would say they are 1/16 of an inch at most. I'd say one of them is about ten inches in length an the other is about 6. The ribbon like structures appear to be only on the surface of the leaf. On the back side of the leaf they are barely visible. On the left side of the leaf there is an odd shaped hole. There is a yellowing around the edge of this hole. It has the shape of a fidget spinner. There appear to be fine, hairlike structures on the stem of the leaf. The stem is more of a yellow green than the rest of the leaf. There are small almost shiny dots on the leaf that go away after it is washed.
The specimen is a serrated edged leaf. The leaf is approximately 155mm in length with an elliptical shape. One end has the base of the stem where the leaf was attached to the mother plant. The other end is pointed. At the widest part, the leaf measures about 50mm. The stem is about 5mm across. There appear to be 2 lighter green "tracks" on the leaf. They take on a drizzled appearance. Almost as if someone drizzled icing on the leaf. The widest part of these tracks measures approximately 2mm at the thinnest part the track measures less than .5mm. These tracks only appear on the right vertical half of the leaf. They only appear on the top surface of the leaf. The length of the tracks in total measure about 105mm and 145mm. On the left vertical half of the leaf there is an oddly shaped hole that has the shape of a fidget spinner. This hole has yellowing around the edges and is about 70mm up from the base of the stem.

Exploratory Data Analysis

Submitted by sbrewer on Fri, 03/08/2019 - 11:00

 

  • 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...

Making Figures with Inkscape

Submitted by sbrewer on Fri, 02/09/2018 - 12:02

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!

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