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sift:application:analyse_page [2024/07/17 15:44] – created sgrangersift:application:analyse_page [2024/08/29 15:11] (current) – sgranger
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   * [[Sift:Statistical_Parametric_Mapping:Using_Statistical_Parametric_Mapping_in_Biomechanics|Statistical Parametric Mapping]]   * [[Sift:Statistical_Parametric_Mapping:Using_Statistical_Parametric_Mapping_in_Biomechanics|Statistical Parametric Mapping]]
  
-Both of these analytical tools can be launched from the [[Sift:Application:Toolbar|top toolbar]], which opens the {{:sift_run_pca.png}}[[Sift:Principal_Component_Analysis:Run_PCA_Dialog|PCA Dialog]] and {{:sift_run_spm.png}}[[Sift:Statistical_Parametric_Mapping:Create_GLM_Dialog|GLM Dialog]].+Both of these analytical tools can be launched from the [[Sift:Application:Toolbar|top toolbar]], which opens the {{:sift_run_pca.png?30}}[[Sift:Principal_Component_Analysis:Run_PCA_Dialog|PCA Dialog]] and {{:sift_run_spm.png?30}}[[Sift:Statistical_Parametric_Mapping:Create_GLM_Dialog|GLM Dialog]].
  
-{{:AnalysePage.png}}+{{:AnalysePage.png?1000}}
  
-==== Principal Component Analysis ====+===== Principal Component Analysis =====
  
 The [[Sift:Principal_Component_Analysis:Using_Principal_Component_Analysis_in_Biomechanics|PCA]] page consists of 6 sub-pages related to [[Sift:Principal_Component_Analysis:Using_Principal_Component_Analysis_in_Biomechanics|PCA]]: **Variance Explained, Loading Vector, Workspace Scores, Group Scores, Extreme Plot and PC Reconstruction**, which are located on the bottom of the page. Each of these pages provides unique analysis into a section of PCA. Many aspects of each display are customizable, with the user able to specify line styles, colours, and axis labels among other display features. The [[Sift:Principal_Component_Analysis:Using_Principal_Component_Analysis_in_Biomechanics|PCA]] page consists of 6 sub-pages related to [[Sift:Principal_Component_Analysis:Using_Principal_Component_Analysis_in_Biomechanics|PCA]]: **Variance Explained, Loading Vector, Workspace Scores, Group Scores, Extreme Plot and PC Reconstruction**, which are located on the bottom of the page. Each of these pages provides unique analysis into a section of PCA. Many aspects of each display are customizable, with the user able to specify line styles, colours, and axis labels among other display features.
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 Once you have completed a PCA analysis on some of your data, you can select that instance from the top menu labeled "PCA Results" on all of the PCA sub-pages. Once you have completed a PCA analysis on some of your data, you can select that instance from the top menu labeled "PCA Results" on all of the PCA sub-pages.
  
-=== Variance Explained ===+==== Variance Explained ====
  
-{{:Sift_VarianceExplained.png}}+{{:Sift_VarianceExplained.png?1000}}
  
 The Variance Explained page contains a bar for each principal component (PC) that was calculated. The line along the back of the graph shows the cumulative amount of variance explained. The total variance explained by all of the calculated PCs is written in the top left corner of the graph. The Variance Explained page contains a bar for each principal component (PC) that was calculated. The line along the back of the graph shows the cumulative amount of variance explained. The total variance explained by all of the calculated PCs is written in the top left corner of the graph.
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 Hovering over a bar causes the percentage explained by that specific PC to be displayed on top of the bar. Hovering over the points on the cumulative amount line causes the PC number, the variance explained by that PC and cumulative variance explained to appear beside the point. Hovering over a bar causes the percentage explained by that specific PC to be displayed on top of the bar. Hovering over the points on the cumulative amount line causes the PC number, the variance explained by that PC and cumulative variance explained to appear beside the point.
  
-=== Loading Vector ===+==== Loading Vector ====
  
-{{:Sift_LoadingVector.png}}+{{:Sift_LoadingVector.png?1000}}
  
 The Loading Vector page shows the shape of the variance explained for the selected PC at each point during the plotted cycle (also called the eigenvector). This helps the user to understand if certain PCs are associated with the variance at specific portions of the gait cycle. The Loading Vector page shows the shape of the variance explained for the selected PC at each point during the plotted cycle (also called the eigenvector). This helps the user to understand if certain PCs are associated with the variance at specific portions of the gait cycle.
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 The user can choose to flip the graph along the y-axis. The user can choose to flip the graph along the y-axis.
  
-=== Workspace Scores ===+==== Workspace Scores ====
  
-{{:Sift_WorkspaceScores.png}}+{{:Sift_WorkspaceScores.png?1000}}
  
 The Workspace Scores page produces a scatter plot of subject scores for two selected PCs. The subject score for a selected PC is the distance between the subject's score for the PC and the mean score for that PC. This scatter plot approach can help users to visualize whether specific subjects appear to cluster together in the PC representation space. The Workspace Scores page produces a scatter plot of subject scores for two selected PCs. The subject score for a selected PC is the distance between the subject's score for the PC and the mean score for that PC. This scatter plot approach can help users to visualize whether specific subjects appear to cluster together in the PC representation space.
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 The user can choose to plot the subjects' normalized scores instead of their raw scores. The user can choose to plot the subjects' normalized scores instead of their raw scores.
  
-=== Group Scores ===+==== Group Scores ====
  
-{{:Sift_GroupScores.png}}+{{:Sift_GroupScores.png?1000}}
  
 The Group Scores display shows the group scores for each PC. The group mean score for each PC is plotted as a point in that group's colour and the standard error is illustrated via error bars. The Group Scores display shows the group scores for each PC. The group mean score for each PC is plotted as a point in that group's colour and the standard error is illustrated via error bars.
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 Hovering over an individual scatter point shows the underlying details for that point. Hovering over an individual scatter point shows the underlying details for that point.
  
-=== Extreme Plot ===+==== Extreme Plot ====
  
-{{:Sift_ExtremePlot.png}}+{{:Sift_ExtremePlot.png?1000}}
  
 The curves in the Extreme Plot display show the shape and magnitudes of the selected PC at specified intervals from the average. Within the Extreme Plot display, users can select among many different plot types: The curves in the Extreme Plot display show the shape and magnitudes of the selected PC at specified intervals from the average. Within the Extreme Plot display, users can select among many different plot types:
  
-<code> +  * Mean +/- 1 SD Reconstruction: Shows the mean signal, as well as the reconstructed waveforms at +/- 1 standard deviation for that PC. The reconstructed wave forms are computed by multiplying the Loading Vector for that PC by +/- 1 standard deviation, and adding that to the mean signal. 
-Mean +/- 1 SD Reconstruction: Shows the mean signal, as well as the reconstructed waveforms at +/- 1 standard deviation for that PC. The reconstructed wave forms are computed by multiplying the Loading Vector for that PC by +/- 1 standard deviation, and adding that to the mean signal. +  * Mean +/- 5th and 95th percentile Reconstruction: Shows the mean signal, as well as the 5th and 95th percentiles of the reconstructed signal for that PC. 
-</code> +  * Mean +/- 5th and 95th percentile raw data: Shows the mean signal, as well as the 5th and 95th percentiles of the raw data for the PC. 
- +  * Mean +/- custom percent reconstruction: Shows the mean signal, as well as reconstructed data for the inputted percentiles. 
-<code> +  * Mean +/- custom workspaces: Shows the mean signal, as well as the workspace mean signal for 2 workspaces. 
-Mean +/- 5th and 95th percentile Reconstruction: Shows the mean signal, as well as the 5th and 95th percentiles of the reconstructed signal for that PC. +  * Mean +/- custom value reconstruction: Shows the mean signal, as well as reconstructed data for the inputted scaling factors. 
-</code> +  * Mean +/- Slider: This option animates each PC from -2 standard deviations to +2 standard deviations while showing the mean curve. The animation starts when the user clicks Play in the bottom right corner.
- +
-<code> +
-Mean +/- 5th and 95th percentile raw data: Shows the mean signal, as well as the 5th and 95th percentiles of the raw data for the PC. +
-</code> +
- +
-<code> +
-Mean +/- custom percent reconstruction: Shows the mean signal, as well as reconstructed data for the inputted percentiles. +
-</code> +
- +
-<code> +
-Mean +/- custom workspaces: Shows the mean signal, as well as the workspace mean signal for 2 workspaces. +
-</code> +
- +
-<code> +
-Mean +/- custom value reconstruction: Shows the mean signal, as well as reconstructed data for the inputted scaling factors. +
-</code> +
- +
-<code> +
-Mean +/- Slider: This option animates each PC from -2 standard deviations to +2 standard deviations while showing the mean curve. The animation starts when the user clicks Play in the bottom right corner. +
-</code>+
  
 Some of the plot types allow the user to input additional specifications. In these cases, the Refresh Plot allows the user to apply their settings to the plot and have it update. Some of the plot types allow the user to input additional specifications. In these cases, the Refresh Plot allows the user to apply their settings to the plot and have it update.
  
-=== PC Reconstruction ===+==== PC Reconstruction ====
  
-{{:Sift_PCReconstruction.png}}+{{:Sift_PCReconstruction.png?1000}}
  
 The PC Reconstruction display shows the user what the selected groups'/subjects' underlying data would look like if it were reconstructed from the selected principal components. The PC Reconstruction display shows the user what the selected groups'/subjects' underlying data would look like if it were reconstructed from the selected principal components.
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   * Notice that the coloring here was done by workspace, and not group, as in the previous sub-pages.   * Notice that the coloring here was done by workspace, and not group, as in the previous sub-pages.
  
-=== Context Menu ===+==== Context Menu ====
  
 {{:Sift_PCAContextMenu.png}} {{:Sift_PCAContextMenu.png}}
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-== Colors ==+=== Colors ===
  
-**Background Color**+==Background Color==
  
 {{:Sift_PCAColor.png}} {{:Sift_PCAColor.png}}
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 This option allows the user to change the color of the background. When it is selected the Select Color dialog box, presented on the right will appear. This option allows the user to change the color of the background. When it is selected the Select Color dialog box, presented on the right will appear.
  
-**Label Color**+==Label Color==
  
 This option allows the user to change the color of the labels on the graph. When it is selected the Select Color dialog box, presented on the right will appear. This option allows the user to change the color of the labels on the graph. When it is selected the Select Color dialog box, presented on the right will appear.
  
-**Axes Color**+==Axes Color==
  
 This option allows the user to change the color of the axis on the graph. When it is selected the Select Color dialog box, presented on the right, will appear. This option allows the user to change the color of the axis on the graph. When it is selected the Select Color dialog box, presented on the right, will appear.
  
  
-== Axes ==+=== Axes ===
  
-**Axis**+==Axis==
  
 Depending on the graph being manipulated, there will be differences in the sub menu. The sub-menu items may be: Depending on the graph being manipulated, there will be differences in the sub menu. The sub-menu items may be:
  
-//None// Selecting this option will remove the labels from the x- and y-axis.+//None// Selecting this option will remove the labels from the x- and y-axis. \\
 {{:Sift_PCAAxisEdit.png}} {{:Sift_PCAAxisEdit.png}}
  
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 //Automatic Re-scale// This option brings the graph back to its automatic scaling in the event that the user has zoomed in or out. The same effect can be accomplished by holding down control and shift and left clicking on the graph. //Automatic Re-scale// This option brings the graph back to its automatic scaling in the event that the user has zoomed in or out. The same effect can be accomplished by holding down control and shift and left clicking on the graph.
 //Font...// This option allows the user to set the Font, Font style, Size, and Effects of the labels. //Font...// This option allows the user to set the Font, Font style, Size, and Effects of the labels.
-== Labels ==+=== Labels ===
  
 **Selection Label** This option allows the user to manipulate the x and y-axis. **Selection Label** This option allows the user to manipulate the x and y-axis.
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 //Font...// This option opens a standard font dialogue box. This allows the user to change the font, font style, size, effects including strikeout and underline and writing system. //Font...// This option opens a standard font dialogue box. This allows the user to change the font, font style, size, effects including strikeout and underline and writing system.
  
-== Lines ==+=== Lines ===
  
 **Line Size** This option allows the user to control the size of the lines on the graph. The options range from 1 to 6. **Line Size** This option allows the user to control the size of the lines on the graph. The options range from 1 to 6.
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 **High Line Type** This option controls the type of the line used for the high points of the PC being graphed. The options are None, Dotted and Line. **High Line Type** This option controls the type of the line used for the high points of the PC being graphed. The options are None, Dotted and Line.
  
-== Scatter Plots ==+=== Scatter Plots ===
  
 **Scatter size** This option allows the user to change the size of the points for all scatter plots. **Scatter size** This option allows the user to change the size of the points for all scatter plots.
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 **Bar Size** This option allows the user to change the width of the percentage bar. The options range from size 0.1 to 0.9. **Bar Size** This option allows the user to change the width of the percentage bar. The options range from size 0.1 to 0.9.
  
-== Error Bars ==+=== Error Bars ===
  
 **Error Bar Color** This option allows the user to change the color of the error bar. When it is selected the Select Color dialog box, presented above, will appear. **Error Bar Color** This option allows the user to change the color of the error bar. When it is selected the Select Color dialog box, presented above, will appear.
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 **Error Bar Size** This option allows the user to change the size of the error bar from sizes 1 to 5. **Error Bar Size** This option allows the user to change the size of the error bar from sizes 1 to 5.
  
-== Miscellaneous ==+=== Miscellaneous ===
  
 **Apply style to all** This option allows the user to apply whatever style changes have been made to all of the graphs at once. **Apply style to all** This option allows the user to apply whatever style changes have been made to all of the graphs at once.
  
-==== Statistical Parametric Mapping ====+===== Statistical Parametric Mapping =====
  
 The SPM page consists of 2 sub-pages related to SPM: Mapping, and Statistics, which are both located on the bottom of the page. Both of these pages provides insight into the components of SPM. Many aspects of the display are customizable, with the user able to specify line styles, colours (through the [[Sift:Application:Data_Options_Dialog|Data Options Dialog]]), and axis labels among other display features. The SPM page consists of 2 sub-pages related to SPM: Mapping, and Statistics, which are both located on the bottom of the page. Both of these pages provides insight into the components of SPM. Many aspects of the display are customizable, with the user able to specify line styles, colours (through the [[Sift:Application:Data_Options_Dialog|Data Options Dialog]]), and axis labels among other display features.
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 Once you have defined your GLM (necessary to build an SPM), you can select that instance from the top menu labeled "GLM Results:" on both of the SPM sub-pages. Similarily, once you have defined your SPM (as a part of a GLM), you can select that instance from the top menu labeled "SPM Results:" on both of the SPM sub-pages. Once you have defined your GLM (necessary to build an SPM), you can select that instance from the top menu labeled "GLM Results:" on both of the SPM sub-pages. Similarily, once you have defined your SPM (as a part of a GLM), you can select that instance from the top menu labeled "SPM Results:" on both of the SPM sub-pages.
  
-=== Mapping ===+==== Mapping ====
  
-{{:Sift_SPMMapping_Control.png}}+{{:Sift_SPMMapping_Control.png?1000}}
  
 The mapping sub-page is where you can define and visualize your GLM. The mapping sub-page is where you can define and visualize your GLM.
  
-== Control ==+=== Control ===
  
 The info section of the mapping sub-page is empty if there is no selected GLM. When a GLM has been calculated and is selected, it is populated with the type of grouping done on the GLM (either by group or workspace), as well as the list of what is involved in the grouping (i.e. either the groups or workspaces). The info section of the mapping sub-page is empty if there is no selected GLM. When a GLM has been calculated and is selected, it is populated with the type of grouping done on the GLM (either by group or workspace), as well as the list of what is involved in the grouping (i.e. either the groups or workspaces).
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 Below the info section there is a create GLM button. This button opens the [[Sift:Statistical_Parametric_Mapping:Create_GLM_Dialog|create GLM dialog]], prompting you to define and create a new GLM. Below the info section there is a create GLM button. This button opens the [[Sift:Statistical_Parametric_Mapping:Create_GLM_Dialog|create GLM dialog]], prompting you to define and create a new GLM.
  
-== Visualizations ==+=== Visualizations ===
  
-{{:Sift_SPMMapping_Plot.png}}+{{:Sift_SPMMapping_Plot.png?1000}}
  
 There are 2 visualizations on the mapping sub-page: the regression matrix B and the residual matrix e. There are 2 visualizations on the mapping sub-page: the regression matrix B and the residual matrix e.
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 **Residual Matrix**: This represents the result of calculating the residual matrix. Similarly to the regression matrix, because we are representing groupings with the experimental design matrix, these residuals represent the difference between the traces and their groupings mean value. **Residual Matrix**: This represents the result of calculating the residual matrix. Similarly to the regression matrix, because we are representing groupings with the experimental design matrix, these residuals represent the difference between the traces and their groupings mean value.
  
-=== Statistics ===+==== Statistics ====
  
-{{:Sift_SPMStatistics_Control.png}}+{{:Sift_SPMStatistics_Control.png?1000}}
  
 The statistics page is where you can define and visualize your SPM. The statistics page is where you can define and visualize your SPM.
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-== Control ==+=== Control ===
  
 The threshold controls the p value for which a t threshold is computed. This threshold depends on both the alpha value provided, as well as the "smoothness" of the data within the GLM. Sections above this threshold in the curve can be thought of as "significant". The threshold controls the p value for which a t threshold is computed. This threshold depends on both the alpha value provided, as well as the "smoothness" of the data within the GLM. Sections above this threshold in the curve can be thought of as "significant".
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 Below the info section there is a create SPM button. This button opens the [[Sift:Statistical_Parametric_Mapping:Create_SPM_Dialog|create SPM dialog]], prompting you to define and create a new SPM. Below the info section there is a create SPM button. This button opens the [[Sift:Statistical_Parametric_Mapping:Create_SPM_Dialog|create SPM dialog]], prompting you to define and create a new SPM.
  
-== Visualization ==+=== Visualization ===
  
-{{:Sift_SPMStatistics_Plot.png}}+{{:Sift_SPMStatistics_Plot.png?1000}}
  
 The visualization shows the selected SPM. On the graph, there are red dotted lines representing the significance threshold (controlled by the threshold value). Any regions of the SPM that are outside of the zone defined by the +/- threshold are significant regions (to the significance alpha), and are shaded in to help display so. The visualization shows the selected SPM. On the graph, there are red dotted lines representing the significance threshold (controlled by the threshold value). Any regions of the SPM that are outside of the zone defined by the +/- threshold are significant regions (to the significance alpha), and are shaded in to help display so.
  
-=== Context Menu ===+==== Context Menu ====
  
 The plots in the SPM sub-pages have a limited context menu, similar to that in the [[Sift:Application:Explore_Page#Context_Menu|Explore Page]]. Of note, the options available in this context menu include: The plots in the SPM sub-pages have a limited context menu, similar to that in the [[Sift:Application:Explore_Page#Context_Menu|Explore Page]]. Of note, the options available in this context menu include:
sift/application/analyse_page.1721231088.txt.gz · Last modified: 2024/07/17 15:44 by sgranger