SMHS SciVisualization NetworkViz - Revision history

Pineaumi: /* Footnotes */

2016-05-23T18:03:13Z

‎Footnotes

Pineaumi: /* Example Early-Onset Alzheimer’s Disease */

2016-05-23T18:02:42Z

‎Example Early-Onset Alzheimer’s Disease

Pineaumi: /* GIS/Distortion mapping */

2016-05-23T18:01:26Z

‎GIS/Distortion mapping

Pineaumi: /* Appendix */

2016-05-23T18:00:43Z

‎Appendix

Pineaumi: /* Pathway analysis */

2016-05-23T17:59:15Z

‎Pathway analysis

Pineaumi: /* Social Network Analysis Example */

2016-05-23T17:56:35Z

‎Social Network Analysis Example

Imoubara: /* Circos Connectogram/Table visualization */

2016-05-23T13:35:15Z

‎Circos Connectogram/Table visualization

Imoubara: /* See Next */

2016-05-19T14:30:22Z

‎See Next

Imoubara: /* Background */

2016-05-19T14:08:38Z

‎Background

Imoubara at 19:27, 18 May 2016

2016-05-18T19:27:42Z

← Older revision		Revision as of 18:03, 23 May 2016
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	*<sup>1</sup> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375		*<sup>1</sup> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375
		+	*<sup>2</sup> http://dx.doi.org/10.1111/jon.12252
		+	*<sup>3</sup> http://dx.doi.org/10.4306/pi.2015.12.1.125

	==See Next==		==See Next==

@@ Line 308: / Line 308: @@
 ===Example Early-Onset Alzheimer’s Disease===
-Recent studies examined the Interactions between imaging (Structural Brain Change) and genetics (SNP) biomarkers in Early-Onset Alzheimer's Disease Subjects. Circular representation of the significant SNP-Neuroimaging interactions. The left and right parts of the graph contain the 15-ROI imaging markers and the 20-SNP genotypes, respectively. The strength of the connection between each SNP-ROI pair is presented as a ribbon, whose size, color and location are proportional to -log (p). Clearly, there are a lot of spurious effects (skinny red lines on background) and several significantly strong associations (thicker purple ribbons on foreground), e.g., purple association between SNP_5 (rs7718456) and ROI_10 (L_hippocampus, Volume). SNP: single nucleotide polymorphism, ROI: region of interest.
+Recent studies<sup>2</sup>,<sup>3</sup> examined the Interactions between imaging (Structural Brain Change) and genetics (SNP) biomarkers in Early-Onset Alzheimer's Disease Subjects. Circular representation of the significant SNP-Neuroimaging interactions. The left and right parts of the graph contain the 15-ROI imaging markers and the 20-SNP genotypes, respectively. The strength of the connection between each SNP-ROI pair is presented as a ribbon, whose size, color and location are proportional to -log (p). Clearly, there are a lot of spurious effects (skinny red lines on background) and several significantly strong associations (thicker purple ribbons on foreground), e.g., purple association between SNP_5 (rs7718456) and ROI_10 (L_hippocampus, Volume). SNP: single nucleotide polymorphism, ROI: region of interest.
 <center>[[Image:SMHS_SciVisualization44.png|400px]] </center>

@@ Line 295: / Line 295: @@
   …
-Java Applet: http://www.socr.ucla.edu/htmls/SOCR_Cartograhy.html
+Java Applet: http://www.socr.ucla.edu/htmls/SOCR_Cartograhy.html<BR>
 Activities: http://wiki.stat.ucla.edu/socr/index.php/SOCR_Cartography_Project
 ==Circos Connectogram/Table visualization==

← Older revision		Revision as of 18:00, 23 May 2016
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	</center>		</center>

		+	===Footnotes===

		+	*<sup>1</sup> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

	==See Next==		==See Next==

@@ Line 252: / Line 252: @@
 ==Pathway analysis==
-Pathway analysis   is a technique that reduces complexity and increased explanatory power in studies examining underlying biological structure of differentially expressed genes and proteins.
+Pathway analysis<sup>1</sup> is a technique that reduces complexity and increased explanatory power in studies examining underlying biological structure of differentially expressed genes and proteins.
   # install package

@@ Line 107: / Line 107: @@
   diag(termMatrix)
-  # The matrix product of incidence matrix (B) and it’s transpose B×B^T represents the degrees of all nodes!
+  # The matrix product of incidence matrix (B) and it’s transpose B×B<sup>T</sup> represents the degrees of all nodes!
   # inspect terms numbered 5 to 10
   termMatrix[5:10,5:10]

@@ Line 303: / Line 303: @@
 Circular chord/ribbon diagrams present a mechanism to visualize numeric tables containing information of directional relations. This type of chart visualizes tables in a circular way. Sectors of the plot is union(rownames(mat), colnames(mat)). When there is no rowname or colname, the chart assigns names for it (rows could be auto-named as "R1", "R2", ... and columns may be named as "C1", "C2").
-•	Circos: http://circos.ca
+*Circos: http://circos.ca
-•	R circlize: http://cran.r-project.org/web/packages/circlize/circlize.pdf
+*R circlize: http://cran.r-project.org/web/packages/circlize/circlize.pdf
 ===Example Early-Onset Alzheimer’s Disease===
@@ Line 416: / Line 416: @@
 ===Practice===
 Repeat these charts using the 03_NIPS_Baby_VitK_Shot_DataSummaryAnalysis_March2012_Short.csv dataset (Appendix), https://umich.instructure.com/files/330392/download?download_frd=1
 ==Graphical Workflow Protocol Visualization==

@@ Line 507: / Line 507: @@
-===See Next===
+==See Next==
 * [[SMHS_SciVisualization| Back to the Scientific Visualization section]]
 * [[SMHS| Back to the Scientific Methods for Health Sciences EBook ToC]]

@@ Line 29: / Line 29: @@
   rglplot(g, layout=layout.kamada.kawai(g))
- # Dataset 1: Coappearance network in the novel “les miserablese”.
+Dataset 1: Coappearance network in the novel “les miserablese”.
-  # Alternatively, we can use a directed, weighted network representing the neural network of the nematode
+D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley, Reading, MA (1993).
- # C. Elegans. D. Watts and S. Strogatz, Nature 393, 440-442 (1998). The file celegansneural.gml describes a
- # weighted, directed network where the nodes have been renumbered to be consecutive.
+The data contains the weighted network of coappearances of characters in Victor Hugo's novel "Les Miserables".
- #  Edge weights are the weights given by Watts.
   install.packages("rgl")

@@ Line 69: / Line 69: @@
+  W
-<b>Social Network Analysis Example</b>
+===Social Network Analysis Example===
   # free memory
@@ Line 161: / Line 161: @@
 <center>[[Image:SMHS_SciVisualization43.png|400px]] </center>
-<b>Hands-on activity (oncological primary doctor and a second-opinion)</b>
+===Hands-on activity (oncological primary doctor and a second-opinion)===
 We use some of the Stanford Real Graph Data (http://snap.stanford.edu/data/) or this graph data on cancer patients seen by a primary doctor and a second-opinion doctor, stage of the disease, and diagnostic agreement between primary and secondary oncologist: <b>Primary</b>, <b>Secondary</b>, <b>Stage</b>, <b>DxAgreement</b>
@@ Line 247: / Line 247: @@
   dev.off() #don’t forget to close the device
-===Pathway analysis===
+==Pathway analysis==
 Pathway analysis   is a technique that reduces complexity and increased explanatory power in studies examining underlying biological structure of differentially expressed genes and proteins.
@@ Line 284: / Line 284: @@
   res[1:15,-12]
-<b>GIS/Distortion mapping</b>
+==GIS/Distortion mapping==
   # install the R GISTools package
@@ Line 296: / Line 296: @@
-<b>Circos Connectogram/Table visualization</b>
+==Circos Connectogram/Table visualization==
 Circular chord/ribbon diagrams present a mechanism to visualize numeric tables containing information of directional relations. This type of chart visualizes tables in a circular way. Sectors of the plot is union(rownames(mat), colnames(mat)). When there is no rowname or colname, the chart assigns names for it (rows could be auto-named as "R1", "R2", ... and columns may be named as "C1", "C2").
@@ Line 304: / Line 304: @@
 •	R circlize: http://cran.r-project.org/web/packages/circlize/circlize.pdf
-<b>Example Early-Onset Alzheimer’s Disease</b>
+===Example Early-Onset Alzheimer’s Disease===
 Recent studies examined the Interactions between imaging (Structural Brain Change) and genetics (SNP) biomarkers in Early-Onset Alzheimer's Disease Subjects. Circular representation of the significant SNP-Neuroimaging interactions. The left and right parts of the graph contain the 15-ROI imaging markers and the 20-SNP genotypes, respectively. The strength of the connection between each SNP-ROI pair is presented as a ribbon, whose size, color and location are proportional to -log (p). Clearly, there are a lot of spurious effects (skinny red lines on background) and several significantly strong associations (thicker purple ribbons on foreground), e.g., purple association between SNP_5 (rs7718456) and ROI_10 (L_hippocampus, Volume). SNP: single nucleotide polymorphism, ROI: region of interest.
@@ Line 411: / Line 411: @@
 <center>[[Image:SMHS_SciVisualization46.png|500px]] </center>
-<b>Practice</b>
+===Practice===
 Repeat these charts using the 03_NIPS_Baby_VitK_Shot_DataSummaryAnalysis_March2012_Short.csv dataset (Appendix), https://umich.instructure.com/files/330392/download?download_frd=1
-===Graphical Workflow Protocol Visualization===
+==Graphical Workflow Protocol Visualization==
 (1)	Brain Imaging & Genetics Data:
@@ Line 449: / Line 449: @@
 <center>[[Image:SMHS_SciVisualization48.png|500px]] </center>
-===Appendix===
+==Appendix==
-Neonate Infant Pain Score (NIPS) Data (Vitamin K shots) Dataset
+===Neonate Infant Pain Score (NIPS) Data (Vitamin K shots) Dataset===