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Notched Boxplot (JFreechart)

Vernalis JFreeChart-based plotting nodes version 1.29.0.v202102191243 by Vernalis (R&D), UK

This node generates notched boxplots of categorical data.

The boxplot shows the following:

  • The box shows the interquartile range (IQR; Q1 to Q3)
  • The whiskers show the extent of the 'regular' values - i.e the range of the actual values within 1.5 * IQR of the IQR
  • The mean is shown as an open circle with a cross in, which may or may not be within the box
  • The median is shown as a line crossing the box
  • The notch shows the 95% confidence interval of the median, defined as +/- 1.57 * IQR / sqrt(N), where N is the number of values. The notch is centred on the median, and may extend beyond the ends of the boxes
  • Outliers are shown as 'o' beyond the whiskers. Outliers are in the range 1.5 * IQR to 2 * IQR beyond the IQR
  • Extreme outliers are shown as 'x' beyond the whiskers. Outliers are beyond 2* IQR beyond the IQR
See this page for details and references

The chart is coloured as follows:

If the 2nd Port is null, then the colour is as follows.

  • The outline and whisker are the specified default outline colour
  • If there is a ColorModel on the 1st port for the category column, then the fill is from the colour model
  • If no colormodel, or it is not on the category column, then the fill colour is the specified default fill colour

If the 2nd port is connected, then it must contain a single string column with a colour model associated to it. The column must contain the names of the series columns (Using an Extract Column Header -> Transpose -> Color Manager sequence of nodes achieves this). Now, the colouring is as follows:

Outline & Whisker

  • If there is a ColorModel on the 1st port for the category column, then the outline is from the colour model
  • If no colormodel, or it is not on the category column, then the outline is the default outline colour specified

Fill

  • If there is a single StringCell column in the second table, then the series fill colours come from the color model
  • If not, or for series names not represented, the fill colour is the default fill colour specified.

For general settings of the generated image, see the "General Plot Options" Tab.

Options

Categorical column
A categorical column (String, Integer, Boolean) which forms the x-axis categories
Keep categories in order of input
If checked, then the categories appear on the x-axis in the order they are first encountered in the input table. Otherwise, they are sorted into their natural ordering
Data (Y-Axis) Values
The column(s) containing the series datapoints
Show mean
Should the mean be included on the plot (as an open circle)?
Mean size
The size that the mean should be shown at
Show median
Should the median be included on the plot?
Show notch
Should the notch be shown on the plot?
Notch size
The proportion of the width of the box by which each notch is indented
Horizontal boxes
Plot is rotated so boxes are horizontal
Show legend
Should a legend be included. Legend will show series colours and category colours as appropriate
Ensure outliers on plot
Without this setting, extreme outliers may be missed off the extremes of the plot. Checking this setting ensures the axes are scaled to ensure that all outliers appear
Line Width
The width (thickness) of the whisker lines and box outlines
Whisker Width
The width of the tails of the whiskers, relative to the width of the box
Outlier size
The size of the outliers
Extreme Outlier size
The size of the extreme outliers
Default outline colour
The colour used for lines when no other colour is specified by table colour models
Default fill colour
The colour used for the box fills when no other colou is specified by table colour models

General Plot Options

Type of Image
The type of the created image can either be png or svg. PNGs are mostly smaller, SVGs provide details about plot and the possibility to be changed individually.
Title of Graph
The title of the graph shown above the generated image. If the title is not activated, no title will be shown.
Width of Image (in pixel)
The width of the generated image, not the plot width.
Height of Image (in pixel)
The height of the generated image, not the plot height.
Background Color
The color of the background of the image. Hence this color is used for the area behind and around the plot as well as behind potential axis and legends.
Plot Background Color
The color of the background of the plot. Hence this color is used for the empty space in a plot.
Plot Background Alpha
The transparency of the plot background can be modified using an additional alpha value. An alpha value of 1 does not change the background transparency. Decreasing the alpha value will increase the plot background transparency.
Scale Font Size
Factor changes the font sizes within the JFreeChart view. A value greater the 1 increases all view fonts, a value between 0 and 1 decrease them.

Input Ports

Icon
Data table with at least one categorical column and one numerical column
Icon
Optional table with series colours - see above for further details

Output Ports

Icon
The image of the plot (SVG or PNG)

Views

Boxplot
Boxplot views of the input data

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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