heatmap labels of the cells clusters are squished

[jjyotikataria]

@nturaga @hawrobin @teslajoy @jweiser @SolomonShorser-OICR

Hi everyone, could you please possibly help me out to fix the label spacing issue of the clusters shown by reactomegsa for the single cell data. As shown in the figure, the data label on the x axis is cropped.

[jgriss]

Hi @jjyotikataria,

Any additional parameter passed to the plot_gsva_heatmap function is directly forwarded to the heatmap.2 function.

Unfortunately, even though it's quite powerful, it's still not a great plotting function. Here is the example taken from the single cell analysis vignette showing you how to adapt the main parameters:

plot_gsva_heatmap(gsva_result, 
                  pathway_ids = relevant_pathways, # limit to these pathways
                  margins = c(6,30), # adapt the figure margins in heatmap.2
                  dendrogram = "col", # only plot column dendrogram
                  scale = "row", # scale for each pathway
                  key = FALSE, # don't display the color key
                  lwid=c(0.1,4)) # remove the white space on the left

Essentially, you'll have to play with the margins and lwid parameters to get the settings right for your plot.

More details on the heatmap.2 parameters can be found here.

[jjyotikataria]

@jgriss It worked!!! You saved my time. Thanks a lot.!!!