JMP Statistics Software portal

2015-01-13

++ JMP Statistics Software portal

Getting help in JMP
-From within JMP you have access to the JMP documentation in pdf form. In this case, select Help --> Books --> Basic Analysis.

Process for making a normal heatmap (cell plot) in JMP
-enter data into a table->Graph->Cell plot->choose columns for y response (color)
-Add a colorbar with red triangle->legend. . . a custom smooth colorbar could be made as well by entering many values from the min to the max and making a new heatmap (or just a new column in the same heatmap) out of that.
--The colors for the colorbar can be changed: File->preferences->graphs->click on continuous color theme in color themes->choose a color theme
-JMP can also do heirarchical clustering and then make a heatmap

Process for making a heirarchically clustered heatmap in JMP
-open some data
-use graph cell plot or follow the directions below
-analyze->multivariate methods->cluster
-choose all of the columns you want to be clustered and "cast the selected columns" as the y columns.  click ok
-click the arrow next to heirarchical clustering and choose two way clustering
-right click graph and choose a color theme if you want a different color theme
-If you want to display the cluster order on the original table then click the arrow next to heirarchical clustering and choose save display order.  You can sort the table by the display order if you want.
-Additional notes
--Unfortunately I don't know how to make additional color bar legends to indicate the different types of samples.  Therefore I manually do this with a variety of other programs.
--[What is the plot on the bottom right of the heatmaps in JMP?]

Process for making histogram in JMP
-Analyze->Distribution->choose the y column to analyze->red arrow next to graph->display options->horizontal layout and axis on left->histogram options->choose count axis and set binwidth
-see also: http://www.jmp.com/support/help/The_Distribution_Report.shtml
-What is the red part of the box and whisker plot in a JMP histogram?
--contacted JMP on 01-06-2014d1336: https://mail.google.com/mail/u/0/?ui=2&shva=1#search/jmp/1436943f89148428
--answer: "The red bracket on the box plot is referred to as the shortest half bracket. It is the shortest interval that contains 50% of the data, so it is the most dense 50% of the observations. For normally distributed data, the shortest half would be the same interval as represented by the box (from the 25th to the 75th percentile)."
-What is the diamond part of the box and whisker plot in a JMP histogram?
--"The confidence diamond contains the mean and the upper and lower 95% of the mean. If you drew a line through the middle of the diamond, you would have the mean. The top and bottom points of the diamond represent the upper and lower 95% of the mean."
-See also
--Template for making histogram label for jmp for 65535 array data
---"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2013\11-10-13\template for histogram label for jmp 11-10-13.svg"

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