Gplots Venn
2021年7月7日Register here: http://gg.gg/vao4c
Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as (’bandplot’, ’wapply’), - enhanced versions of standard plots (’barplot2’, ’boxplot2’, ’heatmap.2’, ’smartlegend’), - manipulating colors (’col2hex’, ’colorpanel’, ’redgreen’, ’greenred’, ’bluered’, ’redblue’, ’rich.colors’), - calculating and plotting two-dimensional data summaries (’ci2d’, ’hist2d’), - enhanced regression diagnostic plots (’lmplot2’, ’residplot’), - formula-enabled interface to ’stats::lowess’ function (’lowess’), - displaying textual data in plots (’textplot’, ’sinkplot’), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements (’balloonplot’), - plotting ’Venn’ diagrams (’venn’), - displaying Open-Office style plots (’ooplot’), - plotting multiple data on same region, with separate axes (’overplot’), - plotting means and confidence intervals (’plotCI’, ’plotmeans’), - spacing points in an x-y plot so they don’t overlap (’space’).
As mentioned, following is an easier alternative (especially when you have 2 groups) with the venn function from the gplots library. This only needs a list containing either the row-numbers or the gene-names of the DEGs which is easier (but offers less adjustability to make it prettier).
*Venn Diagram by ggplot2, with really easy-to-use API. yanlinlin82/ggvenn.
*Invisibly returns an object of class ’venn’, containing a matrix of all possible sets of groups, and the observed count of items belonging to each The fist column contains observed counts, subsequent columns contain 0-1 indicators of group intersectionship. copied from asmeurer / r-gplots
In this post, we will learn how to create venn diagrams for gene lists and how to retrieve the genes present in each venn compartment with R.
In this particular example, we will generate random gene lists using the molbiotools gene set generator but you can use your own gene lists if you prefer. Specifically, we will generate a random list of 257 genes to represent those that are upregulated in condition and another list of 1570 genes to represent those that are upregulated in condition B.
Then, we will sort and paste the gene lists in an excel document we will save as randomGeneLists.xlsx.Plot Venn Diagram
Now, let’s load the data into R using the gdata package.Gplots Venn Color
Now you are ready, to review the genes in each section of the venn diagram separately. Alternatively, you can always use Venny web tool that is a great way to start looking at your data and then write a modified version of this R script to make a more exhaustive figure or facilitate downstream analysis in your script.Gplots Venn
Skewed slots in motor. Feel free to leave comments or email me at info@rjbioinformatics.com.
Register here: http://gg.gg/vao4c
https://diarynote.indered.space
Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as (’bandplot’, ’wapply’), - enhanced versions of standard plots (’barplot2’, ’boxplot2’, ’heatmap.2’, ’smartlegend’), - manipulating colors (’col2hex’, ’colorpanel’, ’redgreen’, ’greenred’, ’bluered’, ’redblue’, ’rich.colors’), - calculating and plotting two-dimensional data summaries (’ci2d’, ’hist2d’), - enhanced regression diagnostic plots (’lmplot2’, ’residplot’), - formula-enabled interface to ’stats::lowess’ function (’lowess’), - displaying textual data in plots (’textplot’, ’sinkplot’), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements (’balloonplot’), - plotting ’Venn’ diagrams (’venn’), - displaying Open-Office style plots (’ooplot’), - plotting multiple data on same region, with separate axes (’overplot’), - plotting means and confidence intervals (’plotCI’, ’plotmeans’), - spacing points in an x-y plot so they don’t overlap (’space’).
As mentioned, following is an easier alternative (especially when you have 2 groups) with the venn function from the gplots library. This only needs a list containing either the row-numbers or the gene-names of the DEGs which is easier (but offers less adjustability to make it prettier).
*Venn Diagram by ggplot2, with really easy-to-use API. yanlinlin82/ggvenn.
*Invisibly returns an object of class ’venn’, containing a matrix of all possible sets of groups, and the observed count of items belonging to each The fist column contains observed counts, subsequent columns contain 0-1 indicators of group intersectionship. copied from asmeurer / r-gplots
In this post, we will learn how to create venn diagrams for gene lists and how to retrieve the genes present in each venn compartment with R.
In this particular example, we will generate random gene lists using the molbiotools gene set generator but you can use your own gene lists if you prefer. Specifically, we will generate a random list of 257 genes to represent those that are upregulated in condition and another list of 1570 genes to represent those that are upregulated in condition B.
Then, we will sort and paste the gene lists in an excel document we will save as randomGeneLists.xlsx.Plot Venn Diagram
Now, let’s load the data into R using the gdata package.Gplots Venn Color
Now you are ready, to review the genes in each section of the venn diagram separately. Alternatively, you can always use Venny web tool that is a great way to start looking at your data and then write a modified version of this R script to make a more exhaustive figure or facilitate downstream analysis in your script.Gplots Venn
Skewed slots in motor. Feel free to leave comments or email me at info@rjbioinformatics.com.
Register here: http://gg.gg/vao4c
https://diarynote.indered.space
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