Figures
For information on paper sizes and overlapping axis labels, scroll down to Graphics (Plot Results).
A. Pie Charts
Tools → Plot → Pie Chart
- A new window will appear with the hierarchical data available in the workspace
- Use the drop down arrows to the left of each taxonomic level to find the OTU of interest
Select the name of the OTU, click Add to Pie (upper right of window)
Adjust the display mode using the options in the upper toolbar. See Display for more information.
- To create sub-wedges in the pie chart (e.g., showing sub-taxa within a phylum), select both the phylum and the taxa of interest within the phylum.
- The pie chart is composed only of the groups selected by the user. Therefore, it may not add to 100% unless all the groups are selected. If it is desired that the pie chart sums to 100%, select the taxa which are domain level 1 (e.g., “Bacteria”) and any desired phyla, genera, etc.
Often the minor components of the dataset are not desired in the pie chart, but the user will want to show these as a collapsed “Other” wedge. To do this, select all of the taxa that you want to collapse together, then click Add to Other. A group named “Other” will appear in the table in bold font. Note: All selected taxa must belong to the same parent-level of taxonomy (i.e., they must all share some common higher level of taxonomy). When you click Add to Other, the selected taxa are automatically added to the pie. Taxa included in collapsed “Other” wedge can be viewed by hovering your cursor over “Other”. To remove the “Other” wedge, select “Other” and click Remove from Pie (the taxa is no longer bold and will return to the initial individual items).
- The selected taxon names are displayed in bold font
To remove data, select a bold font group, then click Remove from Pie.
Once all the desired taxa are selected, click Plot
- A new window will appear containing pie chart display options
To display a single pie chart which includes all libraries’ data, select the Total Libraries checkbox. Note: Only the libraries selected by the filter in the current workspace are shown in the figure setup. To plot all libraries in the project, instead of just those selected by the current filter, create the figure within a new workspace with No filter assigned.
- To view a pie chart which includes only one specific library’s data, select the library name in the column
To display a single pie chart which combines data only from the specific libraries selected in the column, select Libraries on Plot
- Up to 16 pie charts (totaled from Total Libraries, Libraries on Plot, and individual libraries) may be created at once
Use the Rows and Columns options at the top of the window to adjust the display format
Click OK to view the pie charts
To add/remove taxa, click Done (upper right corner of pie chart window) to return to the selection table.
To change the display options, click Data (lower right side of pie chart window).
1. Plot Attributes
After generating a plot with the default settings, the user can change the appearance of the plot through the Plot Attributes button on the lower right side of the Plot Results window.
a) Titles / Axes
Click Titles / Axes tab within Plot Attributes pop-up window
- Enter a single title for multi-pie charts
Sorted libraries have one or more metadata tag(s) pre-appended before the library name, separated by a colon. The libraries are then displayed alphabetically first by metadata tag(s), then by library name. If Show Library Name is deselected, the library names after the colon will disappear, but the metadata tag(s) will remain. Note: If libraries are not sorted and do not have metadata tag(s), then deselecting Show Library Name will not drop the library name (to prevent blank axis labels). For more information on sorting libraries, see Display.
When finished, click Apply in upper right corner of window
b) Colors
Click Colors tab within Plot Attributes pop-up window
To pick a different background color, click the “…” button and select a new color from the pop-up display.
- To pick a different wedge color, click on the color and select a new color from the pop-up display.
When finished, click Save in upper right corner of window
c) Pie Chart Legend and Labels
Click Pie Chart tab within Plot Attributes pop-up window
Adjust whether Value, Percentage, and/or Name label the colors represented in the legend
Adjust the legend Separator if desired
Adjust the Legend Location if desired
Adjust whether Value, Percentage, and/or Name label the wedges on the pie chart
Adjust the pie chart label Separator if desired
Adjust the pie chart Label Location if desired
When finished, click Save in upper right corner of window
B. Heatmaps
Tools → Plot → OTU Heatmap
- A new window will appear with the OTU data table
- To limit the number of OTUs displayed in the heatmap:
Select entire dataset by simply clicking Select Range without defining any limiters
- Manual selection: click on desired OTUs
Select range using limiting boxes on toolbar, then click Select Range: In the first box, type the lower bounding limit. In the second box, type the upper bounding limit. Note: The bounding numbers that are selected in the two boxes are dependent upon the current display mode; so keep in mind that if the display mode is in Counts, the bounding numbers will include those OTUs with corresponding counts/integers. However, if the display mode is in % of Total, the bounding numbers will include those OTUs with corresponding percentages of the total dataset.
Click Plot on lower right side of window
- A new window will appear containing a list of the individual libraries
To display a heatmap which includes data from all libraries, make sure all libraries are selected. Note: Only the libraries selected by the filter in the current workspace are shown in the figure setup. To plot all libraries in the project, instead of just those selected by the current filter, create the figure within a new workspace with No filter assigned.
- To view a heatmap which includes only one specific library’s data, select the single library name in the column.
- To view a combination of a few libraries, Ctrl-click the individual library names.
Select Include unselected OTU Names as 'Other' category to place all OTUs that were not selected on the plot setup page in an "other" category at the bottom of the plot.
Click OK to view the heatmap
To add/remove taxa, click Done (upper right corner of heatmap window) to return to the selection table.
To change the included libraries, click Data (lower right side of heatmap window).
1. Plot Attributes
After generating a plot with the default settings, the user can change the appearance of the plot through the Plot Attributes button on the lower right side of the Plot Results window.
a) Titles / Axes
Click Titles / Axes tab within Plot Attributes pop-up window
- Enter desired plot and axis titles into the designated spaces
Sorted libraries have one or more metadata tag(s) pre-appended before the library name, separated by a colon. The libraries are then displayed alphabetically first by metadata tag(s), then by library name. If Show Library Name is deselected, the library names after the colon will disappear, but the metadata tag(s) will remain. Note: If libraries are not sorted and do not have metadata tag(s), then deselecting Show Library Name will not drop the library name (to prevent blank axis labels). For more information on sorting libraries, see Display.
- Adjust axis label rotations as desired
When finished, click Save in upper right corner of window
b) Colors
Click Colors tab within Plot Attributes pop-up window
To pick a different color spectrum, click Change Colors and select a new spectrum from the pop-up display.
Setting the number of color levels is useful when defining a new color spectrum. To add new colors, start with any existing color spectrum, set the number of colors you want to have in the spectrum (Color Levels), then click on each color to change it to the desired color. Color spectrums can have anywhere between 2 and 8 colors blended together.
To reverse the colors, click Flip Colors.
When finished, click Save in upper right corner of window
c) Heatmap Values and Color Bar
Click Heatmap tab within Plot Attributes pop-up window
Deselect Display Heatmap Values to remove the values from the display; specify number of Decimal Places in displayed heatmap values
- Enter desired color bar title
To change the minimum and maximum values that will be displayed, deselect the Autoscale option, then edit the values
When finished, click Save in upper right corner of window
C. Stacked Bar Charts
Tools → Plot → OTU Stacked Bar
- A new window will appear with the OTU data table
- To limit the number of OTUs displayed in the chart:
Select entire dataset by simply clicking Select Range without defining any limiters
- Manual selection: click on desired OTUs
Select range using limiting boxes on toolbar, then click Select Range: In the first box, type the lower bounding limit. In the second box, type the upper bounding limit. Note: The bounding numbers that are selected in the two boxes are dependent upon the current display mode; so keep in mind that if the display mode is in Counts, the bounding numbers will include those OTUs with corresponding counts/integers. However, if the display mode is in % of Total, the bounding numbers will include those OTUs with corresponding percentages of the total dataset.
Click Plot on lower right side of window
A new window will appear containing a list of Stacked Bar Modes and the individual libraries
Select % of Selected to display only the selected data and create bars of 100% based on the relative percentages of the selected OTUs in each bar.
Select % of Total to create an “other” category from the non-selected OTUs and create bars of 100% based on the selected OTUs plus “other” category.
Select Counts to display raw data counts in integers. This mode does not force the bars to 100%.
To display a bar chart which includes all libraries’ data, make sure all libraries are selected. Note: Only the libraries selected by the filter in the current workspace are shown in the figure setup. To plot all libraries in the project, instead of just those selected by the current filter, create the figure within a new workspace with No filter assigned.
- To view a bar chart which includes only one specific library’s data, select the single library name in the column.
- To view a combination of a few libraries, Ctrl-click the individual library names.
Click OK to view the bar chart
To add/remove taxa, click Done (upper right corner of stacked bar window) to return to the selection table.
To change the included libraries, click Data (lower right side of stacked bar window).
1. Plot Attributes
After generating a plot with the default settings, the user can change the appearance of the plot through the Plot Attributes button on the lower right side of the Plot Results window.
a) Titles / Axes
Click Titles / Axes tab within Plot Attributes pop-up window
- Enter desired plot and axis titles into the designated spaces
Sorted libraries have one or more metadata tag(s) pre-appended before the library name, separated by a colon. The libraries are then displayed alphabetically first by metadata tag(s), then by library name. If Show Library Name is deselected, the library names after the colon will disappear, but the metadata tag(s) will remain. Note: If libraries are not sorted and do not have metadata tag(s), then deselecting Show Library Name will not drop the library name (to prevent blank axis labels). For more information on sorting libraries, see Display.
Deselect the Autoscale option if desired; change axis Min/Max/Step Size
- Adjust axis label rotations as desired
When finished, click Save in upper right corner of window
b) Grid
Click Grid tab within Plot Attributes pop-up window
Deselect Show to remove the gridlines from the display
To change the gridline color, click the “…” button, and select a new color from the pop-up display
To pick a different gridline pattern, select a new pattern from the Pattern dropdown menu
When finished, click Save in upper right corner of window
c) Colors
Click Colors tab within Plot Attributes pop-up window
To pick a different background, other, or no data color, click the “…” button and select a new color from the pop-up display.
To reverse the colors, click Flip Colors
- To pick a different color for any of the OTUs, click on the color box and select a new color from the pop-up display.
When finished, click Save in upper right corner of window
d) Stacked Bar Legend and Orientation
Click Stacked Bar tab within Plot Attributes pop-up window
Adjust the orientation of the stacked bars: Horizontal Bars or Vertical Bars
Adjust whether the bars are stacked OTU Names or stacked Libraries
Adjust the Gap Width between each stacked bar if desired (set to 0% to make the bars touch)
Adjust the Legend Location if desired
When finished, click Save in upper right corner of window
D. Manhattan Plots
These are the plots produced by the Two-Part, Two-Proportions, and Wilcoxon tests.
1. Plot Attributes
After generating a plot with the default settings, the user can change the appearance of the plot through the Plot Attributes button on the lower right side of the Plot Results window.
a) Titles / Axes
Click Titles / Axes tab within Plot Attributes pop-up window
- Enter desired plot and axis titles into the designated text boxes
Sorted libraries have one or more metadata tag(s) pre-appended before the library name, separated by a colon. The libraries are displayed alphabetically first by metadata tag(s), then by library name. If Show Library Name is deselected, the library names after the colon will disappear, but the metadata tag(s) will remain. Note: If libraries are not sorted and do not have metadata tag(s), then deselecting Show Library Name will not drop the library name (to prevent blank axis labels). For more information on sorting libraries, see Display.
Deselect the Autoscale option for each axis if desired; change axis Min/Max/Step Size
- Adjust axis label rotations as desired
When finished, click Save in upper right corner of window
b) Grid
Click Grid tab within Plot Attributes pop-up window
Deselect Show to remove the gridlines from the display
To change the gridline color, click the “…” button, and select a new color from the pop-up display
To pick a different gridline pattern, select a new pattern from the Pattern dropdown menu
When finished, click Save in upper right corner of window
c) Colors
Click Colors tab within Plot Attributes pop-up window
To pick a different background color, click the “…” button and select a new color from the pop-up display.
- To pick a different curve color, click on the color and select a new color from the pop-up display.
When finished, click Save in upper right corner of window
d) Manhattan Plot Legend and Labels
Click Curves tab within Plot Attributes pop-up window
Adjust the Legend Location if desired
Adjust the Curve Width if desired
Adjust the Line Marker Width if desired
Adjust the marker Symbol if desired
When finished, click Save in upper right corner of window
E. Notes
Notes were designed to help keep track of your objectives or thoughts for a particular subset of the data. There are three different types of figure-related notes: Plot Setup Notes, Figure Notes, and Figure Legends. There is a Notes button on the plot setup page, as well as Plot Notes and Figure Legends buttons on the Plot Results window.
1. Record Notes
Click the Notes button on the plot setup or plot results page
- Record ideas, trends, mini-experiment thoughts, etc.
Note: Figure Legend notes do not actually appear as legends beneath the associated figure. These notes are intended solely as a place to record what you might say about the figure in a publication.
Click Save
2. Export Notes
File → Export → Notes
- Using the checkboxes across the top of the dialog, select the type of notes to export
Use the checkboxes in the Selected column to pick which workspace's/figure's notes to export
Click Export
- Enter desired output file name and location
Click Save
F. Print
To print a plot, click Print on the lower right side of the Plot Results window
- A print preview window with more options will appear
- The portrait and landscape icons at the top of the dialog can be toggled.
Use the Page Size dropdown to choose from Letter, A1 or Custom. When you first change a page size to A1, Explicet switches to millimeter Units, but you can switch back to inches if you so desire. The opposite is true for a page size of Letter.
When Paper Size is changed, Explicet does not change the Image Size (this may mean that when switching between landscape and portrait, part of the image is off the page). Pull the slider to a smaller value to force it to fit on the page (click Maintain Aspect Ratio to move both sliders together). This was an intentional design decision so that the image size isn’t disrupted, and the user can make the image any size they want.
The Change Page Size button is greyed out unless you have it set to a custom page size and have changed one of the values.
Image Size, Page Size, Units, and orientation are all saved with the figure; the user can save different sizes for exporting versus printing.
Click OK to keep changes
Click Print
Choose a printer and any desired printer settings, then click Print
G. Export
- Explicet can export graphics images in either bit mapped (.bmp) or vector (.ps and .pdf) formats.
Vector formats can be rescaled (made larger or smaller) to any size with software tools like Adobe Illustrator or GIMP (GNU Image Manipulation Program). For simple display at the original size in Microsoft Word or PowerPoint, the .bmp format is fine. For significant changes in aspect ratio, such as when creating an image for a small figure in a publication, Illustrator/GIMP will likely be needed to maintain the relative proportionality of all of the elements of a graphic.
- Note: Explicet’s scaling capability in Print preview is limited to scaling the graphical elements only; the font size is fixed. Illustrator/GIMP is required when both graphical elements and font size need to change in concert.
1. Spreadsheets (Graphics Setup)
- The data that form the basis for any graphic can be exported as a tab-delimited (.txt) file.
Click Export on lower right side of the graphic setup window
- A new pop-up window will appear
- Choose the export format
Select Entire OTU Name to export the full OTU name, regardless of the current display format.
Select Edited OTU Name to export the abbreviated OTU name exactly as it is displayed in the current workspace.
Choose the OTU Name delimiter (character placed between columns)
To format the export so that it is compatible for use with the program, R, select Export to R.
Click OK
- Another pop-up window will appear
- Enter the desired export file name and location
Click Save
2. Graphics (Plot Results)
Graphics output by Explicet may be in either bit-map formats (such as .png) or vector formats (.pdf), which are readily imported by tools such as Microsoft Word, PowerPoint, and Adobe Illustrator.
- Note: When exporting graphics as bit-map's, there is a gray background behind the axes and legends. Ideally, graphics should be exported using the PDF output since they can be resized without losing any detail. If a bit-map version without the gray background is required, read the exported PDF into one of many PDF readers (i.e., Illustrator) that can save the PDF in any bit-map format needed.
Click Export in lower right corner of Plot Results window
- A preview window with more options will appear
- The portrait and landscape icons at the top of the dialog can be toggled.
Use the Page Size dropdown to choose from Letter, A1 or Custom. When you first change a page size to A1, Explicet switches to millimeter Units, but you can switch back to inches if you so desire. The opposite is true for a page size of Letter.
The Custom size was specifically implemented to handle the case where default paper-based page sizes forced axes labels to superimpose during PDF generation.
When Paper Size is changed, Explicet does not change the Image Size (this may mean that when switching between landscape and portrait, part of the image is off the page). Pull the slider to a smaller value to force it to fit on the page (click Maintain Aspect Ratio to move both sliders together). This was an intentional design decision so that the image size isn’t disrupted, and the user can make the image any size they want.
The Change Page Size button is greyed out unless you have it set to a custom page size and have changed one of the values.
Image Size, Page Size, Units, and orientation are all saved with the figure; the user can save different sizes for exporting versus printing.
Click OK to accept changes to the figure without exporting it
Click Export
- Enter the desired export file name and location
- Select the type of file you wish to export (.pdf, .ps, or image options)
Click Save
H. Save as Figure
- Similar to workspaces, figures are saved within the larger project, so they stay linked to the data from which they were created and do not create additional files on your computer.
Click Done in Plot Results window
Click Save as Figure in lower right corner of plot setup window
- Enter the desired figure name
Click OK
1. Open Existing Figure
- There are 2 different ways to open a figure:
1. Tools → Figures
2. Click the Figures button in the upper right corner of the current workspace window.
A pop-up window will open with the list of existing figures and associated data. The column headings can be clicked to re-sort the list of figures according to Plot Type, Filter, Workspace, date Created, etc. From this window, figures can be opened, deleted, or renamed. Figure notes can be viewed by selecting a figure name and clicking the Show Notes button. Double-clicking on a figure name immediately opens the figure in its original workspace. By clicking Open in Different Workspace, the user can open a figure in a workspace other than the one in which it was created; this step preserves the original figure and creates a new figure in the selected workspace. However, if a filter is changed in a workspace, all figures associated with that workspace will be affected.