show region names on plotmarkers

[yamihn]

hi, is it possible to show the names of some regions on the maplot using plotmarkers?
I did it manually as example, and I'm asking if there is an option to do it automatically.

[rcorces]

no this is not available. you are welcome to make your own plots manually from the data stored in the SummarizedExperiment.

[yamihn]

Hello @mitchTwoTimes, I used ggplot. meta_data= [email protected]) list_data= markertest@***.***@list@lista.data) new_df= cbind(meta_data, list_data) View(new_df) new_df$x <- "Log2FC" colnames(new_df)[5] <- "Log2FC" colnames(new_df)[6] <- "Mean" colnames(new_df)[7] <- "FDR" colnames(new_df)[8] <- "Pval" colnames(new_df)[9]<- "MeanDiff" colnames(new_df)[10] <- "AUC" colnames(new_df)[11] <- "MeanBGD" df_filter= dplyr::filter(new_df, FDR < 0.1, abs(Log2FC) > 1) df_filter_mean = dplyr::filter(df_filter, Mean > 0.40000000) new_df$region <- paste(new_df$seqnames, new_df$start, new_df$end, sep = "-") df_filter$region <- paste(df_filter$seqnames, df_filter$start, df_filter$end, sep = "-") df_filter_mean$region <- paste(df_filter_mean$seqnames, df_filter_mean$start, df_filter_mean$end, sep = "-") new_df$color <- "NA" new_df$color <- ifelse((new_df$FDR < 0.1 & abs(new_df$Log2FC) > 1), "red", "grey50") new_df$DE <- ifelse((new_df$FDR < 0.1 & abs(new_df$Log2FC) > 1), "DE", "NOTDE") ggplot(new_df, aes(x=Mean, y=Log2FC)) + geom_point(colour=new_df$color, aes(shape= DE)) + geom_hline(yintercept = 0) + geom_hline(yintercept = 1, linetype = "dotted", size = 1) + geom_hline(yintercept = -1, linetype = "dotted", size = 1) + ggtitle("MA Plot") + ggrepel::geom_label_repel(aes(label = region), data = df_filter_mean, col= "Blue", alpha= 0.6)