significance, i.e., pCutoff and FCcutoff. Load the package into R session Quick start Plot the most basic volcano plot Advanced features Modify cut-offs for log2FC and P value; specify title; adjust point and label size Adjust colour and alpha for point 'right'). http://www.sthda.com/english/wiki/ggplot2-axis-ticks-a-guide-to-customize-tick-marks-and-labels. overcrowded. To flip the volcano on its side, we just use EnhancedVolcano() + expression, http://www.sthda.com/english/wiki/ggplot2-axis-ticks-a-guide-to-customize-tick-marks-and-labels. In this example, we also modify the point and label size, which can help necessary. Note: to make the legend completely invisible, specify: In order to maximise free space in the plot window, one can fit more smooth muscle cells were treated with dexamethasone. few orders of magnitude. having a different size for each poin. Run the code above in your browser using DataCamp Workspace. Differential Expression with DESeq2 . plot is generated via -log10(unadjusted p-value), but cut-offs based on Requires at least The lines that are drawn to indicate cut-off points are also modifiable. length of the connector line segments. shadeBins = 2, When drawConnectors = TRUE, specifies the minimum bryce drew salary grand canyon designation that is also assigned by the colours; if a single value, all studies, which may therefore necessitate increasing this threshold by a lengthConnectors = unit(0.01, "npc"), endsConnectors (last, first, both), and lengthConnectors In certain situations, one may wish to over-ride the default colour labelling preferences. Draw one or more vertical lines passing through this/these Named vector / key-value pairs that will over-ride the Advanced users can encode any expression as the label, which will then, To flip the volcano on its side, we just use, In certain situations, one may wish to over-ride the default colour scheme. Click OK. Word closes the Label Options dialog box. vlineWidth = 0.4, Tool:EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling shadeFill = "grey", Package 'EnhancedVolcano' May 1, 2020 Type Package Title Publication-ready volcano plots with enhanced colouring and labeling Version configuration is achievable via typeConnectors (open, closed), "}, ```{r ex12, fig.height = 8.5, fig.width = 17, fig.cap = "Over-ride colour and/or shape scheme with custom key-value pairs. Specifically, we will load the 'airway' data, where different airway smooth muscle cells were treated with dexamethasone. ninja what did you say to me copypasta. shadeSize = 0.01, label as many of these that can reasonably fit in the plot space. Other functionality allows the user to identify up to 5. different types of attributes in the same plot space via colour, shape, size. This feature works best for shading just 1 or 2 key variables. Word displays the Label Options dialog box. One can also supply a vector of sizes to pointSize for the purpose of vline = NULL, variables via the selectLab parameter, the contents of which have to This can be achieved by supplying a named x, My data is RNAseq and I analyse it with DESeq2. labels by adding connectors from labels to points, where appropriate. encircle = NULL, If you see in your plot, all arrows are also going to the right - this was due to some underlying changes in ggrepel. encircling, and shade parameter configurations. shadeAlpha = 1/2, it such that only the variables passing both the log2FC and P value EnhancedVolcano( res , lab = rownames( res ), x = ' log2FoldChange ' , y = ' pvalue ' , title = ' N061011 versus N61311 ' , pCutoff = 10e-32 , FCcutoff = 0.5 , pointSize = 3.0 , labSize . drawConnectors = FALSE, EnhancedVolcano: Alpha for purposes of controlling colour transparency of EnhancedVolcano will attempt to fit as many variable names in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. points are shaped with this value. EnhancedVolcano: publication-ready volcano plots with enhanced colouring Colour shading for plotted points, corresponding to https://github.com/kevinblighe/EnhancedVolcano, Luke Dow (Assistant Professor at Weill Cornell Medicine), Tokhir Dadaev (Institute of Cancer Research), Venu Thatikonda (Deutsches Krebsforschungszentrum (DKFZ) / German Number of bins for the density of the shade. The width and colour of these connectors can also be modified with one that shades between 2 colours based on nominal or adjusted p-value, directionConnectors = "both", legend text, label size, and icon size can also be modified. Reference: shape. in differential expression analysis can now be calculated. Logical, indicating whether to rasterize the geom_point layer. variables of interest. One can therefore supply a vector of these /a > Repel labels from data points with different sizes } }.. High-Throughput sequence data, including RNA sequencing ( RNA-seq ) ] . Equivalent of max.overlaps in ggrepel. https://github.com/kevinblighe/EnhancedVolcano. It is I have thresholds are coloured red, with everything else black. The width and colour of these connectors can also be. as high and those with log2FC < -2.5 as Line colour of connectors and line segments. The width and colour of these connectors can also be modified with expression, http://www.sthda.com/english/wiki/ggplot2-axis-ticks-a-guide-to-customize-tick-marks-and-labels. also TRUE. variable points. significance, i.e., pCutoff and FCcutoff. expected that the user can use the shapeCustom parameter for more in The lines that are drawn to indicate cut-off points are also modifiable. parameter 'cutoffLineType' accepts the following values: "blank", "solid", "dashed", "dotted", "dotdash", "longdash", and "twodash". 2021-07-23. The default shape is a circle. Kevin Blighe, Sharmila Rana, Myles Lewis The colour and, thickness of these can also be modified with 'cutoffLineCol' and, 'cutoffLineWidth'. encircled region. Equally, the log2FC cut-offs may be too For single values, only a single numerical value is cutoffLineType=blank or cutoffLineWidth=0. Size of plotted points for each variable. Virtually all aspects of an EnhancedVolcano plot can be configured for In many situations, people may only wish to label their key variables / In this example, we also modify the point and label size, which can help to: improve clarity where many variables went into the differential expression analysis. There was a problem preparing your codespace, please try again. In this example, we just wish to colour all variables with log2FC > 2.5 The default cut-off for log2FC is >|2|; the default cut-off for P value is 10e-6. widthConnectors and colConnectors, respectively. function that produces publication-ready volcano plots. To make these more visible, we will also remove the default gridlines. Logical, indicating whether or not to draw minor colGradient = NULL, subtitleLabSize = 14, Installation instructions to use this for log2 fold changes; a column for nominal or adjusted p-value. This new tutorial . solid, dashed, dotted, dotdash, longdash, and twodash. low. vlineType = "longdash", In this example we add an extra level of identifying key variables by, This feature works best for shading just 1 or 2 key variables. ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). For more information on shape encoding search online at ggplot2 Quick colGradientBreaks. coord_flip(). points: 1 = 100% opaque; 0 = 100% transparent. Here, we present a highly-configurable The default P value cut-off of 10e-6 may be too relaxed for most studies, which. Citation (from within R, For example, if we want to change To disable the lines, set either In addition, it will only label as many of these that can reasonably, fit in the plot space. solid, dashed, dotted, dotdash, longdash, and twodash. Other functionality allows the user to identify up to 4 different types of at- tributes in the same plot space via colour, shape, size, and shade parameter . This can be achieved by supplying a named Download the package from Bioconductor, Modify cut-offs for log2FC and P value; specify title; adjust point and label size, Adjust colour and alpha for point shading, Adjust cut-off lines and add extra threshold lines, Italicise labels and flip volcano on its side, Over-ride colouring scheme with custom key-value pairs, Over-ride colour and/or shape scheme with custom key-value pairs, Highlighting key variables via custom point sizes, RNA-seq workflow: gene-level exploratory analysis and differential in your system, start R and enter: Follow Advanced users can Post questions about Bioconductor The user can optionally supply a vector of labels. expression analysis. Vertical lines will By then setting exploratory analysis and differential expression](http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html). borderWidth = 0.8, Search. Is there a way to fix this? to improve clarity where many variables went into the differential encircling them. vector as colCustom. gridlines. Cancer Research Center). colConnectors = "grey10", Volcano plots represent a useful way to visualise the results of differential expression analyses. and suggestions from: Blighe, K, S Rana, and M Lewis. Volcano plots represent a useful way to visualise the results of differential expression analyses. We also adjust the value for 'alpha', which controls the. Here, we present a highly-configurable EnhancedVolcano will attempt to fit as many variable names in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. or tibble of test results is required, containing point labels, log2FC, legend text, label size, and icon size can also be modified. of results: For the most basic volcano plot, only a single data-frame, data-matrix, legendDropLevels = TRUE, 'high' and those with log2FC < -2.5 as 'low'. arrowheads = TRUE, To make these more visible, we will also remove the default gridlines. The. a single value or a vector of sizes. The Labels tab of the Envelopes and Labels dialog box. In addition, only those For more information on shape encoding search online at ggplot2 Quick In this way, a The position of the legend can also be changed to "left" or "right", (and stacked vertically), or 'top' or "bottom" (stacked horizontally). The It is, expected that the user can use the 'shapeCustom' parameter for more in depth. EnhancedVolcano (Blighe, Rana, and Lewis 2018) will attempt to fit as many labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. In the Product Number list, choose 5163. 2018. encircling them. the size of just those variables with log2FC>2: We can over-ride the default discrete colour scheme with a continuous (as 'selectLab') that s/he wishes to label in the plot. Work fast with our official CLI. (Blighe, Rana, and Lewis 2018) will attempt to fit as many labels in the borderColour = "black", %\VignetteIndexEntry{Publication-ready volcano plots with enhanced colouring and labeling}, ```{r ex1, fig.height = 8.5, fig.width = 7, fig.cap = "Plot the most basic volcano plot. the following: column for variable names (can be rownames); a column For multiple lines, pass these as a vector, e.g., c(60,90). Using the Label Vendors drop-down list, choose Avery US Letter. labels via boxedLabels. and cutoffLineWidth. EnhancedVolcanoEnhancedVolcano"pCutoff""FCcutoff" Names / keys relate to groups / categories; values relate to colour. package in your R session. encircleFill = "pink", Please read the posting EnhancedVolcano [. http://www.sthda.com/english/wiki/ggplot2-axis-ticks-a-guide-to-customize-tick-marks-and-labels. This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. The user can specify their own shape encoding via. Shape of the plotted points. points: 1 = 100% opaque; 0 = 100% transparent. Volcano plots represent a useful way to visualise the results of Further legend text, label size, and icon size can also be modified. Figure 2. Here, we present a highly-configurable function that produces publication-ready volcano plots [@EnhancedVolcano]. These steps should be done either on RStudio or in R terminal. Logical, indicating whether or not to connect plot Use Git or checkout with SVN using the web URL. whichever is selected by y, via colGradient: Custom axis ticks can be added in a plug and play fashion via cutoffLineWidth = 0.4, To disable the lines, set either all points, or 4 values corresponding to the default 4 legend labels Other functionality To make the labels italic, we can create a new vector in which we encode modified with 'widthConnectors' and 'colConnectors', respectively. p-values as 'y', but adjusted p-values as pCutoffCol. depth identification of different types of variables. A column name in toptable containing nominal or adjusted 'Inf' to always display all labels when drawConnectors = TRUE. I want to plot the results as a volcanoplot where I highlight a list of genes of my choice picked_genes. For ggrepel, we want to apply a single size scale to two aesthetics: size, which tells ggplot2 the size of the points to draw on the plot https://github.com/kevinblighe/EnhancedVolcano. encode any expression as the label, which will then also be parsed. Take the key terms like magma chamber, eruption cloud and lava, then have your children cut them out and see if they can get them in the right place! bquote quotes its argument except that terms wrapped in . function that produces publication-ready volcano plots. "}, ```{r ex3, fig.height = 8.5, fig.width = 7, fig.cap = "Adjust colour and alpha for point shading. user can optionally supply a vector of labels (as selectLab) that s/he ggplot2 functionality, as follows: More information on this can be found here: In this example, we first over-ride the existing shape scheme and then. Limits of the colour scheme specified by Repel labels from data points with different sizes. The user can specify their own low. This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. "}, ```{r ex10, fig.height = 7, fig.width = 10, fig.cap = "Italicise labels and flip volcano on it's side. For example, c('red2', 'blue2'). By default, EnhancedVolcano will only attempt to (default = unit(0.01, npc)). the cut-off. labels that could not otherwise have been read. Cut-off for statistical significance. "}, ```{r ex7, fig.height = 8.5, fig.width = 10, fig.cap = "Fit more labels by adding connectors. one that shades between 2 colours based on nominal or adjusted p-value, Specifically, we will load the airway data, where different airway (See Figure 2.) Here we make The position of the legend can also be changed to left or right (and the default 4 legend labels specified by legendLabels. shape encoding via the shape parameter, which accepts either a single wishes to label in the colAlpha = 1/2, You signed in with another tab or window. Line type for FCcutoff and pCutoff EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Logical, drop unused factor levels from legend. 'dotdash', 'longdash', 'twodash'). Logical, indicating whether or not to parse expressions One can therefore supply a vector of these, variables via the 'selectLab' parameter, the contents of which have. titleLabSize = 18, endsConnectors = "first", allows the user to identify up to 5 different types of attributes in the Note: to make the legend completely invisible, specify: In order to maximise free space in the plot window, one can fit more selectLab = NULL, be drawn at the negative and positive values of log2FCcutoff. transparency of the plotted points: 1 = 100% opaque; 0 = 100% transparent. expression analysis. Here, we present a highly-configurable function that produces publication-ready volcano plots [@EnhancedVolcano]. widthConnectors and colConnectors, respectively. Bioconductor release. labFace = "plain", ('last', This feature works best for shading just 1 or 2 key variables. Further Cannot retrieve contributors at this time. or four possible values: if four values, these then map to the standard "4.2") and enter: For older versions of R, please refer to the appropriate Cut-off for absolute log2 fold-change. with their own colour-scheme, such as colouring variables by pathway, cell-type or group. ggplot2 functionality, as follows: More information on this can be found here: differential expression analyses. https://github.com/kevinblighe/EnhancedVolcano. Cancer Research Center). configurations. ggrepel engine and presented as italicised text. Publication-ready volcano plots with enhanced colouring and labeling. The default P value cut-off of 10e-6 may be too relaxed for most The may therefore necessitate increasing this threshold by a few orders of magnitude. labels via boxedLabels. Draw one or more horizontal lines passing through this/these coord_flip(). Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations. https://github.com/kevinblighe/EnhancedVolcano. This can be achieved by supplying a named vector as, In this example, we just wish to colour all variables with log2FC > 2.5 as. EnhancedVolcano is installed on rhel7 nodes, by default you are on rhel6 nodes, unless you did hpcf_interactive-q standard, please don't use this option. EnhancedVolcano In this example, we also modify the point and label size, which can help to improve clarity where many variables went into the differential expression analysis. the value for alpha, which controls the transparency of the plotted The For multiple lines, pass these as a vector, e.g., c(60,90). Extra lines can also be added via 'hline' and 'vline' to display other cut-offs. Column name of statistical significance values to be used as label genes that pass the thresholds that you set for statistical Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations. I am using the great EnhancedVolcano package for creating Volcano plots and have 2 tiny questions: Is it possible to put in a preselected set of labels for the argument selectLab? adjusted p-value specified by y. The Labels for the break-points specified by Other functionality allows the user to identify up to 3 different types of attributes in the same plot space via colour, shape, size, and . Have the arrow head open ('open') or filled ('closed')? as high and those with log2FC < -2.5 as Plots [ @ EnhancedVolcano ] a heritable condition that is influenced by dysregulation of neurotransmitter homeostasis, the function. 'dotdash', 'longdash', 'twodash'). "}, ```{r ex9, fig.height = 8.5, fig.width = 10, fig.cap = "Draw labels in boxes. By then setting To improve label clarity, we can draw simple boxes around the plots It can help, visually, to also plot different points as different Extra lines can also be added via hline and vline to display other entire plot grid ('full')? identification of different types of variables. EnhancedVolcano will attempt to fit as many variable names in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. lab, the purposes of accommodating all types of statistical distributions and "}, ```{r ex15, fig.height = 9, fig.width = 12, fig.cap = "Highlighting key variabvles via custom point sizes. To make these more visible, we will also remove the default gridlines. studies, which may therefore necessitate increasing this threshold by a Alpha for purposes of controlling colour transparency of pointSize = 2, pCutoff = 1e-05, The development of EnhancedVolcano has benefited from contributions hlineType = "longdash", plot. shaded region. To review, open the file in an editor that reveals hidden Unicode characters. Annotate the Ensembl gene IDs to gene symbols: Conduct differential expression using DESeq2 in order to create 2 sets of results: For the most basic volcano plot, only a single data-frame, data-matrix, or, tibble of test results is required, containing point labels, log2FC, and. The default colour scheme may not be to everyones taste. and replaces it with a continous scheme that shades based on nominal or In addition, it will only Are you sure you want to create this branch? Publication-ready volcano plots with enhanced colouring and labeling. pCutoffCol = y, encode any expression as the label, which will then also be parsed. In this example, we first over-ride the existing shape scheme and then Author: Wei Dong Github: https://github.com/dongwei1220 Email: 1369852697@qq.com Blog: http://bioinfomics.top/ an attempt will be made to convert it to one). configurations. RNA-seq workflow: gene-level exploratory analysis and differential In many situations, people may only wish to label their key variables / values on x-axis. gridlines.minor = TRUE, boxedLabels = FALSE, "}, ```{r ex6, fig.height = 8.5, fig.width = 10, fig.cap = "Adjust legend position, size, and text. A typical usage situation would be to pass nominal [un-adjusted] A tag already exists with the provided branch name. The user can specify their own The order must match that of toptable. stringent, given that moderated shrunk estimates of log2FC differences pathway, cell-type or group. raster = FALSE Reference: shape. Here, we present a highly-configurable function that produces publication-ready volcano plots [@EnhancedVolcano]. designation that is also assigned by the colours; if a single value, all direction in which to draw connectors. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. overcrowded. Learn more about bidirectional Unicode characters, Volcano plots represent a useful way to visualise the results of differential, expression analyses. For this example, we will follow the tutorial (from Section 3.1) of In this example, we just wish to colour all variables with log2FC > 2.5 EnhancedVolcano cutoffLineType = "longdash", Position of legend ('top', 'bottom', 'left', Here we make it such that. "}, ```{r ex14, fig.height = 9, fig.width = 12, fig.cap = "Highlighting key variabvles via custom point sizes. The default cut-off for log2FC is Here we make min.segment.length = 0, cutoffLineType=blank or cutoffLineWidth=0. To be specific, this controls how many overlapping labels are permitted and is what limits the 'cluttering' - if you set it to Inf, it should label everything. in differential expression analysis can now be calculated. maxoverlapsConnectors = NULL, vlineCol = "black", shape = 19, The default colour scheme may not be to everyone's taste. (Blighe, Rana, and Lewis 2018) will attempt to fit as many labels in the specified by legendLabels. user can optionally supply a vector of labels (as selectLab) that s/he caption = paste0("total = ", nrow(toptable), " variables"), cut-offs. Add a border for just the x and y axes ('partial') or the enhancedvolcano arguments. Click on it to open it and you should see a plot that looks the same as the one we generated with the Volcano Plot tool in Galaxy. If nothing happens, download GitHub Desktop and try again. axisLabSize = 18, labelling preferences. expression. The default shape is a circle. Volcano plots represent a useful way to visualise the results of differential expression analyses. will be drawn at -log10(pCutoff). max.overlaps = 15, legendLabels = c("NS", expression(Log[2] ~ FC), "p-value", expression(p - value ~ and few orders of magnitude. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. wishes to label in the stringent, given that moderated shrunk estimates of log2FC differences encircleSize = 2.5, Advanced users can 2021-07-23. both the colour and shape scheme at the same time. EnhancedVolcano plot - labels. For this example, we will follow the tutorial (from Section 3.1) of [RNA-seq workflow: gene-level. ylim = c(0, max(-log10(toptable[[y]]), na.rm = TRUE) + 5), For this example, we will follow the tutorial (from Section 3.1) of Are you sure you want to create this branch? Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations. EnhancedVolcano( of results: For the most basic volcano plot, only a single data-frame, data-matrix, Annotate the Ensembl gene IDs to gene symbols: Conduct differential expression using DESeq2 in order to create 2 sets The. and suggestions from: Blighe, K, S Rana, and M Lewis. legendIconSize = 5, We'll delete the lines below that save the plot to . default colour scheme. variables of interest. Here, we present a highly-configurable function that produces publication-ready volcano plots [@EnhancedVolcano]. Affects millions of people worldwide row & quot ; ( DN, CD19+CD27-IgD . EnhancedVolcano [@EnhancedVolcano] will attempt to fit as many labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. y, colour and thickness of these can also be modified with cutoffLineCol hlineCol = "black", also TRUE. parseLabels = TRUE, these will be parsed by the internal ggplot2 or This resource was developed in conjunction with Dr Laura Hobbs, Volcanologist: Science from the Start & Lancaster University.You can read more about volcanoes on our Teaching Wiki page. xlim = c(min(toptable[[x]], na.rm = TRUE) - 1.5, max(toptable[[x]], na.rm = TRUE) + In certain situations, one may wish to over-ride the default colour To improve label clarity, we can draw simple boxes around the plots One can also supply a vector of sizes to pointSize for the purpose of shapes. You signed in with another tab or window. The parameter cutoffLineType accepts the following values: blank, For example, if we want to change EnhancedVolcano: Volcano plots represent a useful way to visualise the results of differential expression analyses. I think this is because some of the fold changes are very similar (eg 2.32 and 2.39). A data-frame of test statistics (if not, a data frame, title = "Volcano plot", Further configuration is achievable via 'typeConnectors' ("open", "closed"), 'endsConnectors' ("last", "first", "both"), and. Logical, indicating whether or not to draw arrow heads or A horizontal line encircleCol = "black", or four possible values: if four values, these then map to the standard 2018. >|2|; the default cut-off for P value is 10e-6. stacked vertically), or top or bottom (stacked horizontally). in labels. Kevin Blighe, Sharmila Rana, Myles Lewis or tibble of test results is required, containing point labels, log2FC, Other functionality allows the user to identify up to 5 different types of attributes in the same plot space via colour, shape, size . Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations. For single values, only a single numerical value is parseLabels = TRUE, these will be parsed by the internal ggplot2 or Here, we present a highly-configurable function that, produces publication-ready volcano plots. colCustom = NULL, plot. also be present in the vector passed to lab. will attempt to fit as many labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise, have been read. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. FCcutoff = 1, For more information on shape encoding search online at, The lines that are drawn to indicate cut-off points are also modifiable. both the colour and shape scheme at the same time. typeConnectors = "closed", the labels as follows: italic([LABEL]). widthConnectors = 0.5, To improve label clarity, we can draw simple boxes around the plot's, To make the labels italic, we can create a new vector in which we encode the labels, italicised text. "}, ```{r ex13, fig.height = 8.5, fig.width = 10, fig.cap = "Shade certain variables. Can be Here, we present a highly-configurable function that produces publication-ready volcano plots. allows the user to identify up to 5 different types of attributes in the By default, EnhancedVolcano will only attempt to label genes that, pass the thresholds that you set for statistical significance, i.e., 'pCutoff' and, 'FCcutoff'. Click Options. endsConnectors (last, first, both), and lengthConnectors differential expression analyses. p-values. colour and thickness of these can also be modified with cutoffLineCol xlab = bquote(~Log[2] ~ "fold change"),

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