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.
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)