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Makes MA plots for each comparison in the results data frame

Usage

plot_MA(
  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 single ggplot object (1 comparison) or a list with ggplot objects.

Examples

se <- prepare_se(report.pg_matrix, expDesign, report.pr_matrix)

#> Imputing along margin 2 (samples/columns).
#> [1] 0.3066195
#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#>  mean imputation used for these rows
#> Cluster size 5574 broken into 3662 1912 
#> Cluster size 3662 broken into 1462 2200 
#> Done cluster 1462 
#> Cluster size 2200 broken into 1110 1090 
#> Done cluster 1110 
#> Done cluster 1090 
#> Done cluster 2200 
#> Done cluster 3662 
#> Cluster size 1912 broken into 1379 533 
#> Done cluster 1379 
#> Done cluster 533 
#> Done cluster 1912 
se <- add_median_peptide_intensity(se)
res <- get_DEPresults(se, type = 'all')
#> Tested contrasts: neg_ctrl_vs_motif1, neg_ctrl_vs_motif2, motif1_vs_motif2
MAplots <- plot_MA(res)