own list: will download either the list from 'own list' or 'manual' based on the 'Type of output' parameter in the sidebar
Download filtered Tableown list: will download either the list from 'own list' or 'manual' based on the 'Type of output' parameter in the sidebar
Download filtered TableIf order of file is ID, logFC, P-value sort column to sort by logFC by 2 and 4 or p-value by 3 and 5
This is the README.md file containing information on the features of the application.
Please contact: Chen.Li@monash.edu or Kerry.Mullan1@monash.edu to report errors.
If using the local GitHub, run the following command in R or Rstudio to download and install the required packages.
install.packages("devtools")
devtools::install_github("KerryAM-R/ggVolcanoR")
ggVolcanoR::runApp()
If the application does not install the dependencies, run the following lines of code
install.packages(c("tidyverse", "ggplot2", "ggrepel", "shiny", "shinyBS", "gridExtra", "DT", "plyr", "dplyr", "reshape2","colourpicker","devtools"), type="source")
devtools::install_github("jokergoo/ComplexHeatmap")
you may need to install Rtools (windows)
The file must contain headers: ID, logFC and Pvalue.
Unique ID names are preferred especially when labelling the graph.
This needs to be in the form of either a .csv or .txt file.
See the test-data format in the GitHub repository or download by setting the significance thresholds to 0.
This includes Arial (Default), Times New Roman and Courier.
Thresholds for significance can be altered (Default: Pvalue=0.05 and absolute logFC=0.58).
These are represented by the horizontal and vertical dotted lines on the graph (Default=grey).
Type in y-axis label which could be:
Axis
Axis tick marks
Font size (range 0 to 100)
For each of the datapoints, the colour, shape, size and transparency
The “range of genes” and “own list” have up to 6 colors to differentiate the points.
The legend can be altered in the following ways:
The title of the graph can be changed for export purposes
The user can also download these features if desired for future reference.
The graph will be exported with the current user defined parameters.
There are two download options:
PDF (default: height=8 and width=10)
png (default assumes legend is present at the 1200 by 1600; recommended to change to 1200 by 1200)
Based on the labelling option selected the table will show the following:
No labels - all imported gene IDs
Range of genes - top 1-x dysregulated genes
Own list - user defined list of genes
The table includes links to several databases:
UniProt 16 species (UniProt_species)
UniProt other species (UniProt_other)
The summary table contains the total number of differentially expressed genes (no labels and range of genes) or the number of significant and non-significant ID's in the list
The following filtered data lists can be downloaded as .csv files (note that significance is based on user defined parameters):
Auguie, B., A. Antonov and M. B. Auguie (2017). “gridExtra: Miscellaneous Functions for "Grid” Graphics. R package version 2.3. https://CRAN.R-project.org/package=gridExtra.“
Bailey, E. (2015). "shinyBS: twitter bootstrap components for Shiny. R package version 0.61. https://CRAN.R-project.org/package=shinyBS.”
Chang, W., J. Cheng, J. Allaire, Y. Xie and J. McPherson (2020). “shiny: Web Application Framework for R. R package version 1.5.0. https://CRAN.R-project.org/package=shiny.”
Slowikowski, K. (2020). ggrepel: Automatically Position Non-Overlapping Text Labels with’ggplot2’.
Villanueva, R. A. M. and Z. J. Chen (2019). ggplot2: Elegant graphics for data analysis, Taylor & Francis.
Wickham, H. (2007). “Reshaping data with the reshape package.” Journal of statistical software 21(12): 1-20.
Wickham, H. (2011). “The split-apply-combine strategy for data analysis.” Journal of statistical software 40(1): 1-29.
Wickham, H., M. Averick, J. Bryan, W. Chang, L. D. A. McGowan, R. François, G. Grolemund, A. Hayes, L. Henry, J. Hester, M. Kuhn, T. L. Pedersen, E. Miller, S. M. Bache, K. Müller, J. Ooms, D. Robinson, D. P. Seidel, V. Spinu, K. Takahashi, D. Vaughan, C. Wilke, K. Woo and H. Yutan (2019). Welcome to the tidyverse, Welcome to the tidyverse. 4: 1686.
Wickham, H., R. François, L. Henry and K. Müller (2020). dplyr: a grammar of data manipulation.
Xie, Y., J. Cheng and X. Tan (2020). DT: A Wrapper of the JavaScript Library “DataTables”.
This is the README.md file containing information on the features of the application.
Please contact: Chen.Li@monash.edu or Kerry.Mullan@monash.edu to report errors.
If using the local GitHub, run the following command in R or Rstudio to download and install the required packages.
install.packages(c("tidyverse", "ggplot2", "ggrepel", "shiny", "shinyBS", "gridExtra", "DT", "plyr", "dplyr", "reshape2"))
The file must contain headers: ID, logFC and Pvalue.
Unique ID names are preferred especially when labelling the graph.
This needs to be in the form of either a .csv or .txt file.
The test-data includes 'proteomics.csv' and 'Transcriptomics.csv' files from Gonglaves et al. (2021)
This includes Arial (Default), Times New Roman and Courier.
The user can changed the x- and y-axis label.
They can also change the cut-offs (p-value and logFC) that may be unique to each dataset.
The user can select the colour, shape, size and transparancy of the datapoints.
There are 4 categories that can be labelled: up/down (overlap of all significant in the same logFC), opposite (logFC is oppostie directions) and other.
The correlation line colours and 95%CI colour can be changed
Like the Volcano plot the user can show where the legend will be placed.
The graph will be exported with the current user defined parameters.
There are two download options:
PDF (default: height=8 and width=10)
png (default assumes legend is present at the 1200 by 1600; recommended to change to 1200 by 1200)
There are only a few features in the bar graph.
All the adjustable parameters, apart from the cut-offs and importing the files, are located above the graph.
Auguie, B., A. Antonov and M. B. Auguie (2017). “gridExtra: Miscellaneous Functions for "Grid” Graphics. R package version 2.3. https://CRAN.R-project.org/package=gridExtra.“
Bailey, E. (2015). "shinyBS: twitter bootstrap components for Shiny. R package version 0.61. https://CRAN.R-project.org/package=shinyBS.”
Chang, W., J. Cheng, J. Allaire, Y. Xie and J. McPherson (2020). “shiny: Web Application Framework for R. R package version 1.5.0. https://CRAN.R-project.org/package=shiny.”
Slowikowski, K. (2020). ggrepel: Automatically Position Non-Overlapping Text Labels with’ggplot2’.
Villanueva, R. A. M. and Z. J. Chen (2019). ggplot2: Elegant graphics for data analysis, Taylor & Francis.
Wickham, H. (2007). “Reshaping data with the reshape package.” Journal of statistical software 21(12): 1-20.
Wickham, H. (2011). “The split-apply-combine strategy for data analysis.” Journal of statistical software 40(1): 1-29.
Wickham, H., M. Averick, J. Bryan, W. Chang, L. D. A. McGowan, R. François, G. Grolemund, A. Hayes, L. Henry, J. Hester, M. Kuhn, T. L. Pedersen, E. Miller, S. M. Bache, K. Müller, J. Ooms, D. Robinson, D. P. Seidel, V. Spinu, K. Takahashi, D. Vaughan, C. Wilke, K. Woo and H. Yutan (2019). Welcome to the tidyverse, Welcome to the tidyverse. 4: 1686.
Wickham, H., R. François, L. Henry and K. Müller (2020). dplyr: a grammar of data manipulation.
Xie, Y., J. Cheng and X. Tan (2020). DT: A Wrapper of the JavaScript Library “DataTables”.
Mullan, K. A. et al. ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets. Comput Struct Biotechnol J 19, 5735-5740, doi:10.1016/j.csbj.2021.10.020 (2021).
Link to publication: https://www.sciencedirect.com/science/article/pii/S2001037021004426