R code or ggplot object to generate high quality heatmap externally

mars · July 16, 2024, 6:00pm

Hello,

I have generated maaslin2 output file including heatmap, however, the quality of heatmap figure is poor. I need to regenerate heatmap externally with high resolution for publication purpose. I checked visualization source code but I am unable to run that code externally.

Could you please guide me on how to use maaslin2 table to produce high quality heatmap?

Many thanks in advance!

nearinj · July 17, 2024, 12:20am

Hi @mars

I would take a look at the source code below for an idea on how the heat map is generated.

github.com

biobakery/Maaslin2/blob/master/R/viz.R#L71


      
                  axis.line.x = ggplot2::element_line(colour = 'black', size = .25),
                  axis.line.y = ggplot2::element_line(colour = 'black', size = .25),
                  panel.border = ggplot2::element_blank(),
                  panel.grid.major = ggplot2::element_blank(),
                  panel.grid.minor = ggplot2::element_blank())
             )
          }
          
          
          # MaAsLin2 heatmap function for overall view of associations
          maaslin2_heatmap <-
              function(
                  output_results,
                  title = NA,
                  cell_value = 'qval',
                  data_label = 'data',
                  metadata_label = 'metadata',
                  border_color = 'grey93',
                  color = colorRampPalette(c("darkblue", "grey90", "darkred")),
                  col_rotate = 90,
                  first_n = 50) {

However, the pdf version of the heatmap shouldn’t suffer from quality issues since its a vector file that you could then export to any DPI/resolution that you need.

Thanks,
Jacob Nearing

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R code or ggplot object to generate high quality heatmap externally

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