DEcompare()

Adrià Mitjavila Ventura

Load plotmics

# load plotmics
library(plotmics)

Run DEcompare()

DEcompare() draws an ggplot2-based scatter plot comparing the log2FC of 2 different differential expression contrasts contrasts.

Required

As input, DEcompare() takes a list of 2 data frames with the columns Geneid, padj.

# read the dataframes into a list
deg_list <- list.files("../testdata", "diff_exp", full.names = T, recursive = T) %>%
  purrr::set_names(paste("cond", 1:3, sep = "")) %>%
  purrr::map(~read.delim(.x))

deg_list[[1]] %>% head()

##   Geneid               ENSEMBL log2FoldChange         padj           DEG
## 1 Gsdmc2 ENSMUSG00000056293.12           2.69 9.334654e-29   Upregulated
## 2 Gsdmc4 ENSMUSG00000055748.12           2.66 1.060432e-28   Upregulated
## 3   Car4 ENSMUSG00000000805.18           2.11 1.883150e-25   Upregulated
## 4 Duoxa2  ENSMUSG00000027225.7           2.97 2.097922e-22   Upregulated
## 5  Neat1  ENSMUSG00000092274.3          -2.25 2.097922e-22 Downregulated
## 6 Gsdmc3 ENSMUSG00000055827.13           2.51 9.601422e-20   Upregulated

Minimum run

DEcompare(deg_list = deg_list[1:2])

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

Change thresholds

DEcompare(deg_list = deg_list[1:2], threshold = 0.1)

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

Customize plot

Change axis limits

DEcompare(deg_list = deg_list[1:2], xlim = c(-5,5), ylim = c(-5, 7))

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

Specify titles

DEcompare(deg_list = deg_list[1:2], main = "This is a title", subtitle = "This is a subtitle", 
            xlab = "This is the X-axis label", ylab = "This is the Y-axis label")

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

Change corner colors

DEcompare(deg_list = deg_list[1:2], color_corners = c("Gray50", "Gray70", "Gray90", "White"))

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

DEcompare(deg_list = deg_list[1:2], color_corners = c("White"))

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

DEcompare(deg_list = deg_list[1:2], alpha_corners = c(1, .1, .4, .7))

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

DEcompare(deg_list = deg_list[1:2], alpha_corners = .2)

## Warning: Removed 7041 rows containing missing values (`geom_point()`).

Further costumization

Since DEcompare() outputs a ggplot2-based scatter plot, it can be further customized with scales or theme, etc.