Plotting DGE on R
Good night!
I'm trying to make a plot of my DGE through R from NOISeq + ComplexHeatmap packages.
I have two dataframes, on the first i have the samples as columns and transcripts as rows. On the seocnd dataframe i have the DGE filtered by p, log2FC, means and theta value.
I already make a plot with all my list, but i can' filter the data then plot only the differentially expressed genes.
If i plot directly the DGE data.frame, he is following the colnames (log2fc, theta, prob and means), i want to use the filtered data and make a heatmap based on log to better visualize their pattern of expression.
Here is how i proceed to plot all my data.frame
mat = mynoiseq2[sample(nrow(mynoiseq.deg), nrow(mynoiseq.deg)), colnames(mynoiseq2)]
hb = HeatmapAnnotation(barplot = anno_boxplot(mat2))
hc = HeatmapAnnotation(barplot = anno_points(rnorm(10))
mat_scaled = t(apply(mat, 1, scale))
Heatmap(mat_scaled, col=rev(rainbow(10)), show_row_names=FALSE, show_column_names=TRUE, column_title_side="top",cluster_columns=FALSE, cluster_rows=FALSE, bottom_annotation = hb, top_annotation=hc, column_title="TSH")
I just want to use the filtered data or filter and normalize.
I'm trying to make a plot of my DGE through R from NOISeq + ComplexHeatmap packages.
I have two dataframes, on the first i have the samples as columns and transcripts as rows. On the seocnd dataframe i have the DGE filtered by p, log2FC, means and theta value.
I already make a plot with all my list, but i can' filter the data then plot only the differentially expressed genes.
If i plot directly the DGE data.frame, he is following the colnames (log2fc, theta, prob and means), i want to use the filtered data and make a heatmap based on log to better visualize their pattern of expression.
Here is how i proceed to plot all my data.frame
mat = mynoiseq2[sample(nrow(mynoiseq.deg), nrow(mynoiseq.deg)), colnames(mynoiseq2)]
hb = HeatmapAnnotation(barplot = anno_boxplot(mat2))
hc = HeatmapAnnotation(barplot = anno_points(rnorm(10))
mat_scaled = t(apply(mat, 1, scale))
Heatmap(mat_scaled, col=rev(rainbow(10)), show_row_names=FALSE, show_column_names=TRUE, column_title_side="top",cluster_columns=FALSE, cluster_rows=FALSE, bottom_annotation = hb, top_annotation=hc, column_title="TSH")
I just want to use the filtered data or filter and normalize.