scRNAtoolVis

https://junjunlab.github.io/scRNAtoolVis-manual/
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scRNAtoolVis is an R package for visualizing single-cell RNA sequencing data with elegant plots...
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### Install scRNAtoolVis Package

Source: https://junjunlab.github.io/scRNAtoolVis-manual/intro.html

Install the development version of the scRNAtoolVis package using devtools. Ensure devtools is installed first.

```r
# install.packages("devtools")
devtools::install_github("junjunlab/scRNAtoolVis")
```

--------------------------------

### Load and Prepare Marker Data

Source: https://junjunlab.github.io/scRNAtoolVis-manual/markervocalno.html

Loads marker gene data from a CSV file and prepares it for plotting. Ensure the 'scRNAtoolVis' package is installed to access example data.

```r
test <- system.file("extdata", "pbmc.markers.csv", package = "scRNAtoolVis")
markers <- read.csv(test)
```

--------------------------------

### View jjDotPlot Help

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Access the help documentation for the jjDotPlot function to see all available arguments and their descriptions.

```r
?jjDotPlot
```

--------------------------------

### Load Test Data for jjVolcano

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Loads the pbmc.markers dataset, which is used as test data for the jjVolcano function. Displays the first few rows to show the data structure.

```R
library(scRNAtoolVis)

# test
data('pbmc.markers')

# check
head(pbmc.markers,3)
```

--------------------------------

### Visualize Gene Expressions with Tiles

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using tiles instead of points, with gene names, a dendrogram, and rescaled expressions. Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          xtree = T,
          rescale = T,
          rescale.min = 0,
          rescale.max = 1,
          point.geom = F,
          tile.geom = T)
```

--------------------------------

### Visualize Marker Genes with Tree Position and Labels

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a marker gene data frame, with celltype annotations, adjusted plot margins, and custom tree position and label settings. Requires the 'pbmc' object and the 'top3pbmc.markers' data frame.

```R
jjDotPlot(object = pbmc,
          markerGene = top3pbmc.markers,
          anno = T,
          plot.margin = c(3,1,1,1),
          tree.pos = 'left',
          same.pos.label = T)
```

--------------------------------

### Load Test Data

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Loads a sample Seurat object for testing the scRNAtoolVis package.

```r
library(scRNAtoolVis)

# load test data
test <- system.file("extdata", "seuratTest.RDS", package = "scRNAtoolVis")
tmp <- readRDS(test)
```

--------------------------------

### Visualize Marker Genes

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a provided marker gene data frame. Requires the 'pbmc' object and the 'top3pbmc.markers' data frame.

```R
jjDotPlot(object = pbmc,
          markerGene = top3pbmc.markers)
```

--------------------------------

### Visualize Gene Expressions with Gene Names

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a provided list of gene names. Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene)
```

--------------------------------

### AverageHeatmap with Custom Annotation Colors

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Applies custom colors to cluster annotations using 'annoCol = TRUE' and 'myanCol'. Requires the 'scales' and 'ggsci' libraries for color palettes.

```r
# change annotation color
library("scales") 
library(ggsci)

mycol <- hue_pal()(9)
mycol1 <- pal_npg()(9)

# plot
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               annoCol = TRUE,
               myanCol = mycol) +
  AverageHeatmap(object = pbmc,
                 markerGene = markers$gene,
                 annoCol = TRUE,
                 myanCol = mycol1)
```

--------------------------------

### Visualize Marker Genes with Dendrogram

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a marker gene data frame and adds a dendrogram to the genes. Requires the 'pbmc' object and the 'top3pbmc.markers' data frame.

```R
jjDotPlot(object = pbmc,
          markerGene = top3pbmc.markers,
          xtree = T)
```

--------------------------------

### Visualize Marker Genes as Heatmap

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a marker gene data frame as a heatmap, with celltype annotations and adjusted plot margins. Requires the 'pbmc' object and the 'top3pbmc.markers' data frame.

```R
jjDotPlot(object = pbmc,
          markerGene = top3pbmc.markers,
          anno = T,
          plot.margin = c(3,1,1,1),
          point.geom = F,
          tile.geom = T)
```

--------------------------------

### Visualize Gene Expressions with Dendrogram

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions with gene names and adds a dendrogram to the genes using the 'xtree' argument. Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          xtree = T)
```

--------------------------------

### Visualize Marker Genes with Celltype Annotation

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a marker gene data frame, adds celltype annotations, and adjusts plot margins. Requires the 'pbmc' object and the 'top3pbmc.markers' data frame.

```R
jjDotPlot(object = pbmc,
          markerGene = top3pbmc.markers,
          anno = T,
          plot.margin = c(3,1,1,1))
```

--------------------------------

### Visualize Gene Expressions with Celltype Annotation

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using gene names and annotates cells by 'celltype'. Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          id = 'celltype')
```

--------------------------------

### Basic jjVolcano Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Generates a basic volcano plot using the loaded pbmc.markers data. This is the default visualization.

```R
# plot
jjVolcano(diffData = pbmc.markers)
```

--------------------------------

### Load Data for AverageHeatmap

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Loads the necessary RDS object and marker gene CSV file for use with AverageHeatmap. Ensure these files are accessible.

```r
httest <- system.file("extdata", "htdata.RDS", package = "scRNAtoolVis")
pbmc <- readRDS(httest)

# load markergene
markergene <- system.file("extdata", "top5pbmc.markers.csv", package = "scRNAtoolVis")
markers <- read.table(markergene, sep = ',', header = TRUE)
```

--------------------------------

### Rescale Gene Expressions with Dendrogram

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions with gene names, adds a dendrogram, and rescales the expressions to a specified range (0 to 1). Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          xtree = T,
          rescale = T,
          rescale.min = 0,
          rescale.max = 1)
```

--------------------------------

### Split Gene Expression Visualization by Groups

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions across multiple groups using the 'split.by' argument and custom dot colors. Requires the 'pbmc' object, a vector of gene names, and 'celltype' annotation.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          id = 'celltype',
          split.by = 'groups',
          dot.col = c('#0099CC','#CC3333'))
```

--------------------------------

### FeatureCornerAxes with Specified Corner Position

Source: https://junjunlab.github.io/scRNAtoolVis-manual/featurecorneraxes.html

Demonstrates how to specify the corner position using the 'axes' and 'cornerVariable' arguments. Two plots are generated with different corner variables and then combined.

```r
p1 <- FeatureCornerAxes(object = tmp,reduction = 'umap',
                        groupFacet = 'orig.ident',
                        relLength = 0.5,
                        relDist = 0.2,
                        aspect.ratio = 1,
                        features = c("Actb","Ythdc1", "Ythdf2"),
                        axes = 'one')

p2 <- FeatureCornerAxes(object = tmp,reduction = 'umap',
                        groupFacet = 'orig.ident',
                        relLength = 0.5,
                        relDist = 0.2,
                        aspect.ratio = 1,
                        features = c("Actb","Ythdc1", "Ythdf2"),
                        axes = 'one',
                        cornerVariable = 'ST4')

# combine
cowplot::plot_grid(p1,p2,ncol = 2,align = 'hv')
```

--------------------------------

### Split UMAP Plot with Cell Labels and Theme

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Creates a faceted UMAP plot with cell labels, no legend, and a 'bwCorner' theme. Facets by 'orig.ident'.

```r
# split
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = "cellType",
                  groupFacet = 'orig.ident',
                  noSplit = F,
                  cellLabel = T,
                  cellLabelSize = 3,
                  show.legend = F,
                  aspect.ratio = 1,
                  themebg = 'bwCorner')
```

--------------------------------

### Rescale Gene Expressions with Custom Color Scale

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions with gene names, a dendrogram, and rescales expressions to a range of -2 to 2 with a custom color scale centered at 0. Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          xtree = T,
          rescale = T,
          dot.col = c('blue','white','red'),
          rescale.min = -2,
          rescale.max = 2,
          midpoint = 0)
```

--------------------------------

### Load Test Data

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Loads the scRNAtoolVis package and test data, then adds group and celltype information to the object. Also loads marker gene data.

```R
library(scRNAtoolVis)

httest <- system.file("extdata", "htdata.RDS", package = "scRNAtoolVis")
pbmc <- readRDS(httest)

# add groups
pbmc$groups <- rep(c('stim','control'),each = 1319)
# add celltype
pbmc$celltype <- Seurat::Idents(pbmc)

# load markergene
data("top3pbmc.markers")

# check
head(top3pbmc.markers,3)
```

--------------------------------

### Split Gene Expression Heatmap by Groups

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions as a heatmap across multiple groups, with AES grouping turned off. Requires the 'pbmc' object, a vector of gene names, and 'celltype' annotation.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          id = 'celltype',
          split.by = 'groups',
          split.by.aesGroup = T,
          point.geom = F,
          tile.geom = T)
```

--------------------------------

### AverageHeatmap with Custom Colors

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Customizes the heatmap colors using the 'htCol' argument. Provide a vector of valid color strings.

```r
# change color
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               htCol = c("#339933", "#FFCC00", "#FF0033"))
```

--------------------------------

### Order Genes in Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions with a custom gene order, reversing the default order. Requires the 'pbmc' object and a vector of gene names.

```R
# change gene order
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          gene.order = rev(top3pbmc.markers$gene))
```

--------------------------------

### Split Gene Expression Visualization by Groups (AES Group Off)

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions across multiple groups, with AES grouping turned off. Requires the 'pbmc' object, a vector of gene names, and 'celltype' annotation.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          id = 'celltype',
          split.by = 'groups',
          split.by.aesGroup = T)
```

--------------------------------

### UMAP Plot with Custom Theme

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Applies a 'bwCorner' theme to the UMAP plot and adjusts corner text size.

```r
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5,
                  cornerTextSize = 2,
                  themebg = 'bwCorner')
```

--------------------------------

### jjVolcano Plot with Text and Fontface Arguments

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Customizes the appearance of gene text labels in the volcano plot by passing arguments like size and fontface, which are forwarded to geom_text_repel.

```R
# cluster label arguments passed to geom_text_repel
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdBu', 15)[4:12],
          size  = 3.5,
          fontface = 'italic')
```

--------------------------------

### AverageHeatmap with Custom Dimensions

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Adjusts the width and height of the heatmap using the 'width' and 'height' arguments. Useful for controlling the plot's aspect ratio and size.

```r
# change heatmap width and height
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               clusterAnnoName = F,
               width = 8,height = 16)
```

--------------------------------

### Change Point Shape in Gene Expression Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions with gene names, adds a dendrogram, rescales expressions, and changes the point shape. Requires the 'pbmc' object and a vector of gene names.

```R
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          xtree = T,
          rescale = T,
          rescale.min = 0,
          rescale.max = 1,
          point.shape = 22)
```

--------------------------------

### Default AverageHeatmap Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Generates a default AverageHeatmap using the loaded object and marker genes. This provides a basic visualization of average expression.

```r
# plot
AverageHeatmap(object = pbmc,
               markerGene = markers$gene)
```

--------------------------------

### Default UMAP Plot with Corner Axes

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Generates a default UMAP plot with corner axes. Set noSplit to TRUE for a single plot.

```r
# umap
clusterCornerAxes(object = tmp,reduction = 'umap',
                  noSplit = T)
```

--------------------------------

### Adjust Annotation Position in Marker Gene Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Visualizes gene expressions using a marker gene data frame, with celltype annotations, adjusted plot margins, custom tree position, label settings, and a specific y-axis position for annotations. Requires the 'pbmc' object and the 'top3pbmc.markers' data frame.

```R
jjDotPlot(object = pbmc,
          markerGene = top3pbmc.markers,
          anno = T,
          plot.margin = c(3,1,1,1),
          tree.pos = 'left',
          same.pos.label = T,
          yPosition = 10.3)
```

--------------------------------

### Generate Vocalno Plot for Marker Genes

Source: https://junjunlab.github.io/scRNAtoolVis-manual/markervocalno.html

Generates a vocalno plot using the markerVocalno function. Specify the number of top genes to display and customize the label colors.

```r
markerVocalno(markers = markers,
              topn = 5,
              labelCol = ggsci::pal_npg()(9))
```

--------------------------------

### FeatureCornerAxes with Custom Color Bar Range

Source: https://junjunlab.github.io/scRNAtoolVis-manual/featurecorneraxes.html

Illustrates setting a custom value range for the color bar in FeatureCornerAxes plots. Two plots are generated, one with default range and another with 'minExp' and 'maxExp' set, then combined.

```r
p1 <- FeatureCornerAxes(object = tmp,reduction = 'umap',
                        groupFacet = NULL,
                        relLength = 0.5,
                        relDist = 0.2,
                        features = c("Actb","Ythdc1", "Ythdf2"),
                        aspect.ratio = 1,
                        themebg = 'bwCorner')

p2 <- FeatureCornerAxes(object = tmp,reduction = 'umap',
                        groupFacet = NULL,
                        relLength = 0.5,
                        relDist = 0.2,
                        features = c("Actb","Ythdc1", "Ythdf2"),
                        aspect.ratio = 1,
                        themebg = 'bwCorner',
                        minExp = 0,maxExp = 2)

# combine
cowplot::plot_grid(p1,p2,ncol = 1,align = 'hv')
```

--------------------------------

### tSNE Plot with Corner Axes

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Generates a corner axes plot using tSNE reduction instead of UMAP. Facets by 'orig.ident'.

```r
# tsne
clusterCornerAxes(object = tmp,
                  reduction = 'tsne',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5)
```

--------------------------------

### jjVolcano Plot with Custom Point Colors

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Modifies the color of the data points in the volcano plot by providing a custom color vector for the aesthetics.

```R
# change point color
jjVolcano(diffData = pbmc.markers,
          aesCol = c('purple','orange'))
```

--------------------------------

### UMAP Plot with Single Axis

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Retains only one corner axis on the left for clarity when faceting by metadata. Requires noSplit = F.

```r
# retain only one axes
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5,
                  axes = 'one')
```

--------------------------------

### AverageHeatmap Marking Specific Genes

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Highlights specific genes on the heatmap by providing a vector of gene names to 'markGenes'. Row names and cluster annotation names are also hidden for clarity.

```r
# mark some genes
# tartget gene
annoGene <- c("LDHB","CCR7","LEF1","NKG7","CST7",
              "GZMK","HLA-DQA1","HLA-DRB1","HLA-DPA1")

AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               clusterAnnoName = F,
               showRowNames = F,
               markGenes = annoGene)
```

--------------------------------

### jjVolcano Plot with Custom Gene List

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Visualizes specific genes of interest within the volcano plot by providing a custom vector of gene names.

```R
# supply own genes
mygene <- c('LTB','CD79B','CCR7','GNLY')

jjVolcano(diffData = pbmc.markers,
          myMarkers = mygene)
```

--------------------------------

### UMAP Plot with Added Circles

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Adds circles to each cluster on the UMAP plot to mark them, with adjustable transparency and binning for circle calculation.

```r
# add circle
clusterCornerAxes(object = tmp,reduction = 'umap',
                  noSplit = T,
                  cornerTextSize = 3.5,
                  themebg = 'bwCorner',
                  addCircle = TRUE,
                  cicAlpha = 0.2,
                  nbin = 200)
```

--------------------------------

### AverageHeatmap without Cluster Annotation Name

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Hides the cluster annotation name displayed on the heatmap by setting 'clusterAnnoName = FALSE'.

```r
# remove cluster anno name
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               clusterAnnoName = F)
```

--------------------------------

### UMAP Plot Faceted by Metadata

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Facets the UMAP plot by a metadata column ('orig.ident') to visualize clusters across different categories. Adjusts aspect ratio and relative length.

```r
# facet by metadata column "orig.ident"
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5)
```

--------------------------------

### UMAP Plot with Legend Key Size Adjustment

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Modifies the size of the legend keys for cluster labels in a UMAP plot.

```r
# legend key size
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = 'cellType',
                  noSplit = T,
                  keySize = 8)
```

--------------------------------

### jjVolcano Plot with Adjusted Cluster Order

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Reorders the clusters displayed in the volcano plot by providing a custom order using the cluster.order argument.

```R
# ajust cluster orders
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('PuOr', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          cluster.order = rev(unique(pbmc.markers$cluster)))
```

--------------------------------

### FeatureCornerAxes Plot Without Legend

Source: https://junjunlab.github.io/scRNAtoolVis-manual/featurecorneraxes.html

Creates a FeatureCornerAxes plot identical to the default but with the legend hidden. Set 'show.legend = F' to omit the legend.

```r
FeatureCornerAxes(object = tmp,reduction = 'umap',
                  groupFacet = 'orig.ident',
                  relLength = 0.5,
                  relDist = 0.2,
                  features = c("Actb","Ythdc1", "Ythdf2"),
                  show.legend = F)
```

--------------------------------

### UMAP Plot with Custom Line Color

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Changes the color of the corner axes lines and labels to 'grey50'.

```r
# line color
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5,
                  lineTextcol = 'grey50')
```

--------------------------------

### UMAP Plot with Cell Type Labels

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Adds cell type labels directly onto the UMAP plot and adjusts label size. Requires noSplit = T.

```r
# add cell type
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = "cellType",
                  noSplit = T,
                  cellLabel = T,
                  cellLabelSize = 5)
```

--------------------------------

### Change Cluster Order in jjDotPlot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjdotplot.html

Use the `cluster.order` argument to specify a custom order for clusters in the dot plot. The `gene.order` argument can be used to reverse the order of genes.

```r
jjDotPlot(object = pbmc,
          gene = top3pbmc.markers$gene,
          gene.order = rev(top3pbmc.markers$gene),
          cluster.order = 8:0,
          ytree = F)
```

--------------------------------

### Default FeatureCornerAxes Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/featurecorneraxes.html

Generates a default FeatureCornerAxes plot with faceting by 'orig.ident'. Use this for a standard visualization of gene expression with corner axes.

```r
FeatureCornerAxes(object = tmp,reduction = 'umap',
                  groupFacet = 'orig.ident',
                  relLength = 0.5,
                  relDist = 0.2,
                  features = c("Actb","Ythdc1", "Ythdf2"))
```

--------------------------------

### Polar jjVolcano Plot with Expanded Y-axis Limits

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Creates a polar volcano plot and then customizes the y-axis limits using ggplot2's ylim() function to expand the range of the plot.

```R
# expand limits
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdYlBu', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          polar = T) +
  ylim(-8,10)
```

--------------------------------

### UMAP Plot with Cell Labels and No Legend

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Displays cell type labels on the UMAP plot while hiding the legend. Requires noSplit = T.

```r
# remove legend
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = "cellType",
                  noSplit = T,
                  cellLabel = T,
                  cellLabelSize = 5,
                  show.legend = F)
```

--------------------------------

### AverageHeatmap without Row Names

Source: https://junjunlab.github.io/scRNAtoolVis-manual/averageheatmap.html

Hides the row names (gene names) in the heatmap by setting 'showRowNames = FALSE'. Useful for cleaner visualizations when gene names are not critical.

```r
# remove rownames
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               showRowNames = F)
```

--------------------------------

### jjVolcano Plot with Custom Rectangle Fill Color

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Changes the fill color of the rectangles that represent clusters in the volcano plot using a specified color palette.

```R
# change cluster rect color
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdBu', 15)[4:12])
```

--------------------------------

### Polar jjVolcano Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Transforms the volcano plot into a polar coordinate system using the 'polar = T' argument, suitable for circular data visualization.

```R
# make a polar plot
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdBu', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          polar = T)
```

--------------------------------

### Flipped jjVolcano Plot

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Rotates the volcano plot by 90 degrees using the 'flip = T' argument, changing the orientation of axes and labels.

```R
# flip the plot
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('PiYG', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          legend.position = c(0.8,0.2),
          flip = T)
```

--------------------------------

### UMAP Plot with Open Arrow Type

Source: https://junjunlab.github.io/scRNAtoolVis-manual/clustercorneraxes.html

Customizes the corner axes plot by changing the arrow type to 'open'.

```r
# arrowType
clusterCornerAxes(object = tmp,reduction = 'umap',
                  noSplit = T,arrowType = 'open')
```

--------------------------------

### Adjust jjVolcano Plot with Cutoffs and Color Type

Source: https://junjunlab.github.io/scRNAtoolVis-manual/jjvolcano.html

Customizes the volcano plot by adjusting the log2 fold change cutoff, specifying the color type based on adjusted p-value, and limiting the number of top genes displayed.

```R
# change aes color type
jjVolcano(diffData = pbmc.markers,
          log2FC.cutoff = 0.5,
          col.type = "adjustP",
          topGeneN = 3)
```

--------------------------------

### FeatureCornerAxes Plot Without Facet Group

Source: https://junjunlab.github.io/scRNAtoolVis-manual/featurecorneraxes.html

Generates a FeatureCornerAxes plot without splitting the plot by group. Set 'groupFacet = NULL' to disable faceting.

```r
FeatureCornerAxes(object = tmp,reduction = 'umap',
                  groupFacet = NULL,
                  relLength = 0.5,
                  relDist = 0.2,
                  features = c("Actb","Ythdc1", "Ythdf2"),
                  aspect.ratio = 1)
```
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