I have reduced several files that the app uses. I outline below the changes:
annotation_annotatr.rds - 331MB ->54.2MB. I filtered to only the rows and columns used.
annotation.rds - 196MB -> 161MB, same as above
I reduced the size of the betas data frame by pre-calculating mean and sd per celltype/trimester. I modified functions to accomodate this new input object betas_summarized.rds
betas.rds - 826 MB,
betas_summarized.rds - 175 MB
Together these changes bring the total object size down below 1gb. I'm not sure if what the usage is during app runtime though.
However, this means that the following features will no longer work:
separate samples by sex,
plot boxplots of specific cpgs
I have not removed these features yet, (users can still see the 'filter by sex' and 'plot individual cpg boxplots' options) they simply will not work. We should remove these though ASAP.
@Yifan-Yin Can you deploy this version onto shinyapps and ensure that it runs under the 1gb limit? I would switch to the free plan to make sure.
I have reduced several files that the app uses. I outline below the changes:
annotation_annotatr.rds- 331MB ->54.2MB. I filtered to only the rows and columns used.annotation.rds- 196MB -> 161MB, same as aboveI reduced the size of the betas data frame by pre-calculating mean and sd per celltype/trimester. I modified functions to accomodate this new input object
betas_summarized.rdsbetas.rds- 826 MB,betas_summarized.rds- 175 MBTogether these changes bring the total object size down below 1gb. I'm not sure if what the usage is during app runtime though.
However, this means that the following features will no longer work:
I have not removed these features yet, (users can still see the 'filter by sex' and 'plot individual cpg boxplots' options) they simply will not work. We should remove these though ASAP.
@Yifan-Yin Can you deploy this version onto shinyapps and ensure that it runs under the 1gb limit? I would switch to the free plan to make sure.