Visualize DMRs - GianlucaMattei/methyl.O GitHub Wiki
Visualize Methylations:
The package includes the option to visualize one or more DMRs occurring on one gene, displaying the features, the corresponding transcripts, the CGIs and the beta differences. The graphic representation helps to better evaluate the effect of the methylated segments on gene expression.
Figure2: Starting from the top of the plot are shown: the chromosome location, the CGIs ranges, the promoter range and its direction, one or more transcripts associated with the gene and the information about the DMR including the beta difference value and length.
R:
To visualize the desired gene, the function plotDMRs needs the resulting annotated list from annotateDMRs and the symbol ID of the gene. Other optional parameters permit to select the database to use between Ensembl and UCSC (annotation), the genome assembly version (hg), the width of the promoter (prom.width), the possibility to show all transcripts or the longest (show.all.transcripts) and to select the genomic range to show (coord.zoom). By this function it is possible to plot the beta values of samples in order to evaluate the methylation levels between two conditions. In this case this information must be included in the annotated list and in the initial input data.frame of ranges. To plot the single beta values for each sample it is necessary to indicate the name of the columns in the initial input data.frame (beta1.name, beta2.name) which can be found also under the column “other” in the annotated list object. For example by using the provided dataset you can use beta1.name=”betaTum”, beta2.name=”betaHlt”. Other graphical parameters permit: - to set the colors of the plotted beta values (beta.colors) if the beta difference value is plotted beta.colors then one color must be specified for beta.colors otherwise two must be chosen, - to set if the output plot should be in greyscale (blackandwhite), - to decide if the plotted range should be zoomed out for a better visualization (smartzoom) and other settings to save the plot including the path (path) the height and width of the output pdf (height.pdf, width.pdf).
plotDMRs(annotatedDMRs,”CTF1”)
GUI:
The tab Visualize Methylation permits to plot the DMR. The main part of the page displays the plot as shown in figure 5. In the left panel are noted the customizable settings
| Command | Description |
|---|---|
| Gene Symbol | The gene symbol to be displayed |
| Beta 1 Name / Beta 2 Name | In order to plot the singles beta values for each sample it is necessary to indicate the name of the columns in the initial input data.frame (beta1.name, beta2.name) which can be found also under the column “other” in the annotated list object |
| Select Beta Color | Sets the color of the beta difference value or the color for beta value for sample 1 |
| Select Beta 2 Color | Sets the color for beta value for sample 2 |
| Show All Transcripts | If TRUE all transcripts are shown for the selected gene |
| Plot in Grayscale | If TRUE the plot will be displayed in grayscale |
| Smart Zoom | Zoom out the range for a better visualization |
| Promoters Length | Sets the promoter length |
| Zoom Coordinate - From / to | Sets custom coordinates for the range to display |