Prepare the data for making MA plots

Prepare the data for making MA plots

Usage

prepare_MA_data(
  res,
  label = NULL,
  ns_color = "grey70",
  up_color = "red3",
  down_color = "dodgerblue"
)

Arguments

res

A data frame with results from get_DEPresults()

label

Specifies which points to label. The default is 'sig', labeling all significant points. Entering a value for top_n limits the labeling to the top_n up- and top_n down-regulated proteins based on the p.adj. When providing a vector with protein names, only those points are labeled.

ns_color

Specifies the color of non-significant proteins.

up_color

Specifies the color of the significantly up-regulated proteins.

down_color

Specifies the color of the significantly down-regulated proteins.

Value

A list with data frames.

Examples

se <- prepare_se(report.pg_matrix, expDesign)

#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#>  mean imputation used for these rows
#> Cluster size 5548 broken into 2203 3345 
#> Cluster size 2203 broken into 1569 634 
#> Cluster size 1569 broken into 1504 65 
#> Cluster size 1504 broken into 645 859 
#> Done cluster 645 
#> Done cluster 859 
#> Done cluster 1504 
#> Done cluster 65 
#> Done cluster 1569 
#> Done cluster 634 
#> Done cluster 2203 
#> Cluster size 3345 broken into 2136 1209 
#> Cluster size 2136 broken into 1087 1049 
#> Done cluster 1087 
#> Done cluster 1049 
#> Done cluster 2136 
#> Done cluster 1209 
#> Done cluster 3345 
se <- add_median_peptide_intensity(se, report.pr_matrix)
res <- get_DEPresults(se, type = 'all')
#> Tested contrasts: neg_ctrl_vs_motif1, neg_ctrl_vs_motif2, motif1_vs_motif2
data <- prepare_MA_data(res)