create_phylogeny_And_heatmap.r - Image labels/size to be dynamically re-adjusted

[nandan75]

Describe the bug

Fontconfig error: No writable cache directories
null device
          1

When the R script create_phylogeny_And_heatmap.r

is run.

To Reproduce run the step create_phylogeny_And_Heatmap_image.nf

Expected behavior Expected The plot combined_plot_mqc.png is created however issues with labels

• I can see the column labels on the top (truncated)
• But the row labels (species) are either not generated or are placed out of the image frame!

Screenshots If applicable, add screenshots to help explain your problem.

Environment (please complete the following information):

• nextflow

Additional context Screenshot 1 : Is expected image as generated outside nextflow (bash pipeline) Screenshot 2 : As generated in nextflow

The datasets (species) are different- so please do not compare the heatmaps :-)

Both images used the same create_phylogeny_And_heatmap.r script

[nandan75]

Tried the following

locate the cache directory using the following command in a terminal:

fc-cache -v
/usr/lib/fontconfig/cache: not cleaning unwritable cache directory

Create a Local Cache Directory

mkdir -p ~/.cache/fontconfig

Set Permissions:

chmod 755 ~/.cache/fontconfig

Set Environment Variable in R script (bin/create_phylogeny_And_heatmap.r):

Sys.setenv(FONTCONFIG_CACHE = "~/.cache/fontconfig")

This DOES NOT CHANGE the image and solve the problem

[nandan75]

• Actually when I checked recreating the phylogeny_heatmap_combined image on my local mac
  • using - Same script and the input gene matrices from the nextflow pipeline, this is mostly an issue with the file format/labels!
• I will revisit this in more details
• The above error is possibly putting me off-track!

[nandan75]

This issue is now identified as more of

• making space available for the heatmap
• Reducing the relative size of the tree branches
• And thus accomodating labels on both rows and columns
• Sorted
• Will push the changes

[nandan75]

Pushed changes

• Issue was found not related to Fontconfig error: No writable cache directories
• It was about printing the labels within the image frame
• The code seems to accomodate multiple sized plots (sample number Rows / AMR gene numbers Columns)
• However the solution can be improved - Some other combination of Row/Columns can possibly push the labels out of the image view!
• To be revisited