### Install ggVolcano Package

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Instructions for installing the development version of the ggVolcano package from GitHub using devtools.

```R
# install.packages("devtools")
devtools::install_github("BioSenior/ggVolcano")
```

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

### Basic gradual_volcano Plot

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Demonstrates the basic usage of the `gradual_volcano` function to create a volcano plot with gradient coloring. Similar to `ggvolcano`, it requires DEG data and allows customization of labels and point sizes. The gradient coloring is applied based on the magnitude of change.

```R
# plot
gradual_volcano(deg_data, x = "log2FoldChange", y = "padj",
                label = "row", label_number = 10, output = FALSE)
```

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

### Customize gradual_volcano Plot Colors

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Illustrates how to customize the fill and color schemes for a gradient volcano plot using `gradual_volcano`. Users can provide color palettes from packages like `RColorBrewer` or `ggsci` to achieve desired visual effects.

```R
library(RColorBrewer)

# Change the fill and color manually:
p1 <- gradual_volcano(data, x = "log2FoldChange", y = "padj",
          fills = brewer.pal(5, "RdYlBu"),
          colors = brewer.pal(8, "RdYlBu"),
          label = "row", label_number = 10, output = FALSE)

p2 <- gradual_volcano(data, x = "log2FoldChange", y = "padj",
          label = "row", label_number = 10, output = FALSE)+
  ggsci::scale_color_gsea()+
  ggsci::scale_fill_gsea()

library(patchwork)
p1|p2

# You can adjust the size range of the points using `pointSizeRange = c(min_size,max_size)`.
```

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

### Basic ggvolcano Plotting

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Generates a standard volcano plot using differential expression data and GO term information. Requires 'deg_data' and 'term_data' dataframes. The plot maps log2 fold change to adjusted p-value, with gene labels.

```r
data("term_data")

# plot
term_volcano(deg_data, term_data,
             x = "log2FoldChange", y = "padj",
             label = "row", label_number = 10, output = FALSE)
```

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

### Basic ggvolcano Plot

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Demonstrates the basic usage of the `ggvolcano` function to create a general volcano plot. It requires a DEG result data frame with columns for GeneName, Log2FC, pValue, and FDR. The `add_regulate` function can be used to add a 'regulate' column if it's missing. Key parameters include the data frame, x-axis (Log2FC), y-axis (FDR), label column, and the number of labels to display.

```R
library(ggVolcano)

## basic example code
# load the data
data(deg_data)

# use the function -- add_regulate to add a regulate column 
# to the DEG result data. 
data <- add_regulate(deg_data, log2FC_name = "log2FoldChange",
                     fdr_name = "padj",log2FC = 1, fdr = 0.05)

# plot
ggvolcano(data, x = "log2FoldChange", y = "padj",
          label = "row", label_number = 10, output = FALSE)
```

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

### Customize ggvolcano Plot Colors

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Shows how to customize the fill and color aesthetics of a volcano plot generated by `ggvolcano`. This can be done manually by providing color vectors or by using external color scales from packages like `ggsci`.

```R
# Change the fill and color manually:
p1 <- ggvolcano(data, x = "log2FoldChange", y = "padj",
          fills = c("#e94234","#b4b4d8","#269846"),
          colors = c("#e94234","#b4b4d8","#269846"),
          label = "row", label_number = 10, output = FALSE)

p2 <- ggvolcano(data, x = "log2FoldChange", y = "padj",
          label = "row", label_number = 10, output = FALSE)+
  ggsci::scale_color_aaas()+
  ggsci::scale_fill_aaas()

library(patchwork)
p1|p2
```

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

### Customize ggvolcano Plot Appearance

Source: https://github.com/biosenior/ggvolcano/blob/main/README.md

Customizes the appearance of the ggvolcano plot, including point fill colors based on gene terms, general point color, and legend background. Utilizes RColorBrewer for color palettes. Dependencies include RColorBrewer.

```r
library(RColorBrewer)

# Change the fill and color manually:
deg_point_fill <- brewer.pal(5, "RdYlBu")
names(deg_point_fill) <- unique(term_data$term)

term_volcano(data, term_data,
             x = "log2FoldChange", y = "padj",
             normal_point_color = "#75aadb",
             deg_point_fill = deg_point_fill,
             deg_point_color = "grey",
             legend_background_fill = "#deeffc",
             label = "row", label_number = 10, output = FALSE)
```

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