My functions to perform the various overrepresentation/enrichment analyses generally assume the result of extract_significant_genes() as the input. Sadly, I do not want to save those data structures to disk because they can be quite monstrously large when serialized (because I keep a reference to the input in them which gets dereferenced on save()). As a result, it is far simpler/safer to just read the xlsx outputs produced by combine_de_tables and extract_significant_genes. Ergo the following two little functions.
<- function(xlsx, sheet = "outcome") {
table_reader <- openxlsx::readWorkbook(xlsx, sheet = sheet, startRow = 2)
input_df rownames(input_df) <- input_df[["row.names"]]
"row.names"]] <- NULL
input_df[[print(dim(input_df))
if (nrow(input_df) < 5000) {
warning("Something appears wrong with the de table: ", input_xlsx)
}return(input_df)
}
<- function(xlsx, sheet = "outcome", direction = "up") {
sig_reader <- paste0(direction, "_deseq_", sheet)
this_sheet <- openxlsx::readWorkbook(xlsx, sheet = this_sheet, startRow = 2)
input_df rownames(input_df) <- input_df[["row.names"]]
"row.names"]] <- NULL
input_df[[dim(input_df)
if (nrow(input_df) < 20) {
message("There are less than 20 rows in this significance table, it is unlikely to be interesting.")
}return(input_df)
}
I have been having some difficulties getting the treeplot fonts to match our readability goals. The set of things I have tried so far are:
With that in mind, the following two parameters are going to set the width and height of the output pdf documents which will be sent to Maria Adelaida in order to arrange into the final figures via inkscape.
<- 6
treeplot_height <- 12
treeplot_width <- 24
wrap_width <- "BP" desired_go_ont
I once again moved the ontology analyses to their own document. This is primarily because I want a fresh notebook to play around with these and get some of the resulting clutter out of the DE notebooks.
The con of doing this is that some of my enrichment methods are smart enough to directly take the output from combine_de_tables()/extract_significant_genes(). I guess I can dispatch a method to take the xlsx file as input…
Thus, for each enrichment analysis that was in the differential expression documents, there will now be a few stanzas here, one which loads the appropriate xlsx file, one which performs gProfiler, and one which uses clusterProfiler. On occasion there may be another with random stuff like me poking at transcription factors or other side interests…
In addition, I am going to do the Tumaco-only analyses first, because they are what are actually in the paper.
The gene set enrichment will follow each DE analysis during this document. I am adding a series of explicitly GSEA analyses in this most recent iteration, in these I will pass the full DE table and check the distribution of logFC values against the genes in each category as opposed to the simpler over-enrichment of the high/low DE genes.
Most (all?) of the gene set enrichment analyses performed in this document are a combination of gProfiler2 (Kolberg et al. (2020)) and clusterProfiler (Yu et al. (2012)). There are functions available in hpgltools to also perform a few other methods, but for the moment I am sticking to only these two. Oh yeah, I need to wrap clusterProfiler’s tree (taken from topGO) plotter because it spams plots everywhere…
<- glue("analyses/3_cali_and_tumaco/DE_Cure_Fail/Clinical_Samples/tc_clinical_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") all_de_cf_table
## [1] 12162 68
<- sig_reader(glue("analyses/3_cali_and_tumaco/DE_Cure_Fail/Clinical_Samples/tc_clinical_cf_sig_sva-v{ver}.xlsx"), "outcome", "up")
all_de_cf_up <- sig_reader(glue("analyses/3_cali_and_tumaco/DE_Cure_Fail/Clinical_Samples/tc_clinical_cf_sig_sva-v{ver}.xlsx"), "outcome", "down")
all_de_cf_down <- rbind.data.frame(all_de_cf_up, all_de_cf_down)
all_de_cf
<- glue("analyses/4_tumaco/DE_Cure_Fail/t_all_visitcf_sig_sva-v{ver}.xlsx")
tumaco_xlsx <- openxlsx::readWorkbook(tumaco_xlsx, sheet = 3, startRow = 2)
t_de_cf rownames(t_de_cf) <- t_de_cf[["row.names"]]
"row.names"]] <- NULL
t_de_cf[[<- t_de_cf[, c("deseq_logfc", "deseq_adjp", "deseq_basemean", "deseq_lfcse")]
t_de_cf_up <- openxlsx::readWorkbook(tumaco_xlsx, sheet = 4, startRow = 2)
t_de_cf rownames(t_de_cf) <- t_de_cf[["row.names"]]
"row.names"]] <- NULL
t_de_cf[[<- t_de_cf[, c("deseq_logfc", "deseq_adjp", "deseq_basemean", "deseq_lfcse")]
t_de_cf_down <- rbind.data.frame(t_de_cf_up, t_de_cf_down) t_de_cf
The following gProfiler searches use the all_gprofiler() function instead of simple_gprofiler(). As a result, the results are separated by {contrast}_{direction}. Thus ‘outcome_down’.
The same plots are available as the previous gProfiler searches, but in many of the following runs, I used the dotplot() function to get a slightly different view of the results.
The xlsx files are:
<- glue("{cf_prefix}/All_Samples/t_clinical_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_clinical_cf_table_sva
## [1] 14156 68
<- glue("{cf_prefix}/All_Samples/t_clinical_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome")
t_clinical_cf_sig_sva_up <- sig_reader(input_xlsx, "outcome", "down") t_clinical_cf_sig_sva_down
And without biopsies
<- glue("{cf_prefix}/All_Samples/t_clinical_nobiop_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_clinicalnb_cf_table_sva
## [1] 11910 68
<- glue("{cf_prefix}/All_Samples/t_clinical_nobiop_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome")
t_clinicalnb_cf_sig_sva_up <- sig_reader(input_xlsx, "outcome", "down")
t_clinicalnb_cf_sig_sva_down <- rbind.data.frame(t_clinicalnb_cf_sig_sva_up,
t_clinicalnb_cf_sig_sva_both t_clinicalnb_cf_sig_sva_down)
After most of the DE analyses, the set of significantly DE genes gets passed to gProfiler2 and clusterProfiler. One slightly neat thing in my gprofiler (and goseq/topGO/gostats) function(s): it coerces the result into the same datastructure produced by clusterProfiler, thus one may play with the various plotting functions in the enrichplot (Yu (n.d.)) package. This is kind of fun because gProfiler2 provides easy access to a few datasets:
My general sense is that the comparisons of primary interest are reactome and one or more GO. I suspect that if there are lots of transcription factors, that might prove interesting.
<- simple_gprofiler(
t_cf_clinical_gp_up
t_clinical_cf_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinical_cure_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinical_gp_up
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_clinical_gp_up[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinical_gp_up' not found
<- sm(enrichplot::treeplot(go_termsim,
t_cf_clinical_gp_go_up_tree label_format = wrap_width))
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinical_gp_up_tree.pdf",
width = treeplot_width, height = treeplot_height)
## Warning in pp(file = "images/overrepresentation/t_cf_clinical_gp_up_tree.pdf",
## : The directory: images/overrepresentation does not exist, will attempt to
## create it.
t_cf_clinical_gp_go_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_go_up_tree' not found
dev.off()
## png
## 2
t_cf_clinical_gp_go_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_go_up_tree' not found
::dotplot(t_cf_clinical_gp_up[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinical_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_clinical_gp_up[["REAC_enrich"]]) reactome_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinical_gp_up' not found
<- sm(enrichplot::treeplot(reactome_termsim,
t_cf_clinical_gp_reac_up_tree label_format = wrap_width))
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'reactome_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinical_gp_up_tree.pdf",
width = treeplot_width, height = treeplot_height)
t_cf_clinical_gp_reac_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_reac_up_tree' not found
dev.off()
## png
## 2
t_cf_clinical_gp_reac_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_reac_up_tree' not found
pp(file = "images/overrepresentation/t_cf_clinical_gp_up_dot.pdf",
width = treeplot_width, height = treeplot_height)
::dotplot(t_cf_clinical_gp_up[["REAC_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinical_gp_up' not found
dev.off()
## png
## 2
::dotplot(t_cf_clinical_gp_up[["REAC_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinical_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_clinical_gp_up[["TF_enrich"]]) tf_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinical_gp_up' not found
## The treeplot fails for this for some reason?
##t_cf_clinical_gp_tf_up_tree <- sm(enrichplot::treeplot(tf_termsim))
::dotplot(t_cf_clinical_gp_up[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinical_gp_up' not found
::dotplot(t_cf_clinical_gp_up[["WP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinical_gp_up' not found
No biopsies!
<- simple_gprofiler(
t_cf_clinicalnb_gp_up
t_clinicalnb_cf_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinicalnb_cure_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinicalnb_gp_up
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_clinicalnb_gp_up[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinicalnb_gp_up' not found
<- sm(enrichplot::treeplot(go_termsim,
t_cf_clinicalnb_gp_go_up_tree label_format = wrap_width))
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "figures/t_cf_clinicalnb_gp_up_tree.svg",
width = treeplot_width, height = treeplot_height)
t_cf_clinicalnb_gp_go_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_go_up_tree' not found
dev.off()
## png
## 2
t_cf_clinicalnb_gp_go_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_go_up_tree' not found
::dotplot(t_cf_clinicalnb_gp_up[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinicalnb_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_clinicalnb_gp_up[["REAC_enrich"]]) reactome_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinicalnb_gp_up' not found
<- sm(enrichplot::treeplot(reactome_termsim,
t_cf_clinicalnb_gp_reac_up_tree label_format = wrap_width))
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'reactome_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinicalnb_gp_up_tree.pdf",
width = treeplot_width, height = treeplot_height)
t_cf_clinicalnb_gp_reac_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_reac_up_tree' not found
dev.off()
## png
## 2
t_cf_clinicalnb_gp_reac_up_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_reac_up_tree' not found
pp(file = "images/overrepresentation/t_cf_clinicalnb_gp_up_dot.pdf",
width = treeplot_width, height = treeplot_height)
::dotplot(t_cf_clinicalnb_gp_up[["REAC_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinicalnb_gp_up' not found
dev.off()
## png
## 2
::dotplot(t_cf_clinicalnb_gp_up[["REAC_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinicalnb_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_clinicalnb_gp_up[["TF_enrich"]]) tf_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinicalnb_gp_up' not found
## The treeplot fails for this for some reason?
##t_cf_clinicalnb_gp_tf_up_tree <- sm(enrichplot::treeplot(tf_termsim))
::dotplot(t_cf_clinicalnb_gp_up[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinicalnb_gp_up' not found
::dotplot(t_cf_clinicalnb_gp_up[["WP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinicalnb_gp_up' not found
The only significant results for this group appear to be GO.
<- simple_gprofiler(
t_cf_clinical_gp_down
t_clinical_cf_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinical_fail_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinical_gp_down
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_down' not found
<- enrichplot::pairwise_termsim(t_cf_clinical_gp_down[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinical_gp_down' not found
<- sm(enrichplot::treeplot(go_termsim)) t_cf_clinical_gp_go_down_tree
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinical_gp_down_tree.pdf",
width = treeplot_width, height = treeplot_height)
t_cf_clinical_gp_go_down_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinical_gp_go_down_tree' not found
dev.off()
## png
## 2
No biopsies!
<- simple_gprofiler(
t_cf_clinicalnb_gp_down
t_clinicalnb_cf_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinicalnb_fail_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinicalnb_gp_down
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_down' not found
<- enrichplot::pairwise_termsim(t_cf_clinicalnb_gp_down[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinicalnb_gp_down' not found
<- sm(enrichplot::treeplot(go_termsim)) t_cf_clinicalnb_gp_go_down_tree
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinicalnb_gp_down_tree.pdf",
width = treeplot_width, height = treeplot_height)
t_cf_clinicalnb_gp_go_down_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_go_down_tree' not found
dev.off()
## png
## 2
t_cf_clinicalnb_gp_go_down_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_go_down_tree' not found
## And both, this is not usually where I put this, but the
## clinical samples are a bit of a special case.
<- simple_gprofiler(
t_cf_clinicalnb_gp_both
t_clinicalnb_cf_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinicalnb_fail_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinicalnb_gp_both
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_both' not found
<- enrichplot::pairwise_termsim(t_cf_clinicalnb_gp_both[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinicalnb_gp_both' not found
<- sm(enrichplot::treeplot(go_termsim)) t_cf_clinicalnb_gp_go_both_tree
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinicalnb_gp_both_tree.pdf",
width = treeplot_width, height = treeplot_height)
t_cf_clinicalnb_gp_go_both_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_go_both_tree' not found
dev.off()
## png
## 2
t_cf_clinicalnb_gp_go_both_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_go_both_tree' not found
<- enrichplot::pairwise_termsim(t_cf_clinicalnb_gp_both[["REAC_enrich"]]) reac_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_clinicalnb_gp_both' not found
<- sm(enrichplot::treeplot(reac_termsim)) t_cf_clinicalnb_gp_reac_both_tree
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'reac_termsim' not found
pp(file = "images/overrepresentation/t_cf_clinicalnb_gp_both_reac_tree.pdf",
width = treeplot_width, height = treeplot_height)
t_cf_clinicalnb_gp_reac_both_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_reac_both_tree' not found
dev.off()
## png
## 2
t_cf_clinicalnb_gp_reac_both_tree
## Error in eval(expr, envir, enclos): object 't_cf_clinicalnb_gp_reac_both_tree' not found
The following essentially repeats the gProfiler2 invocation using clusterProfiler. I have a couple of functions which compare the GO results from various methods, perhaps I should dig it out and see how similar the results are using these two tools. My assumption is that the primary differences should arise from the fact that gProfiler theoretically is updating their GO data over time and cProfiler uses the information in org.Hs.eg.db, which afaik has not changed in quite a while.
<- simple_clusterprofiler(
t_cf_clinical_cp_up de_table = t_clinical_cf_table_sva,
t_clinical_cf_sig_sva_up, excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinical_cure_up_cp-v{ver}.xlsx"))
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
## Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Loading required namespace: Vennerable
##
## Writing the MF data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_clinical_cp_up[["enrich_objects"]][["BP_all"]]) enrichplot
<- simple_clusterprofiler(
t_cf_clinical_cp_down
t_clinical_cf_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Overrepresentation/clinical_fail_up_cp-v{ver}.xlsx"))
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_clinical_cp_down[["enrich_objects"]][["BP_all"]]) enrichplot
GSEA is not associated with either up nor down, it takes the rank order of genes with respect (in this case) to fold-change.
<- plot_topn_gsea(t_cf_clinical_cp_up)
t_cf_clinical_topn_gsea "GO"]][[1]] t_cf_clinical_topn_gsea[[
"GO"]][[2]] t_cf_clinical_topn_gsea[[
"GO"]][[3]] t_cf_clinical_topn_gsea[[
"GO"]][[4]] t_cf_clinical_topn_gsea[[
"GO"]][[5]] t_cf_clinical_topn_gsea[[
The relevant xlsx files are:
<- glue("{xlsx_prefix}/DE_Visits/tv1_vs_later_tables-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "later_vs_first") tv1_vs_later_table
## [1] 11910 68
<- glue("{xlsx_prefix}/DE_Visits/tv1_vs_later_sig-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "later_vs_first")
tv1_vs_later_up_sig <- sig_reader(input_xlsx, "later_vs_first", "down") tv1_vs_later_down_sig
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
I am not likely to do the decreased in visit 1, there are only 7 genes.
<- simple_gprofiler(
tv1later_up_gp
tv1_vs_later_up_sig,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/tv1_vs_later_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
tv1later_up_gp
## Error in eval(expr, envir, enclos): object 'tv1later_up_gp' not found
::dotplot(tv1later_up_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 'tv1later_up_gp' not found
::dotplot(tv1later_up_gp[["REAC_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 'tv1later_up_gp' not found
Note to self: make some classes for plot_topn_gsea so it can handle the various inputs it is likely to receive.
<- simple_clusterprofiler(
tv1later_up_cp de_table = tv1_vs_later_table,
tv1_vs_later_up_sig, orgdb = "org.Hs.eg.db", kegg_prefix = "hs", do_kegg = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
::dotplot(tv1later_up_cp[["enrich_objects"]][["MF_all"]]) enrichplot
::dotplot(tv1later_up_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- write_cp_data(
written
tv1later_up_cp,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/tv1_vs_later_up_cp-v{ver}.xlsx"))
## Writing a sheet containing the legend.
## Writing the MF data.
## Writing the CC data.
## Finished writing excel file.
<- plot_topn_gsea(tv1later_up_cp)
tv1later_topn_gsea "GO"]][[1]] tv1later_topn_gsea[[
"GO"]][[2]] tv1later_topn_gsea[[
The relevant input xlsx files are:
Oh, I messed up and put the DE results in the GSEA directory!
Let us see if we observe general male/female differences in the data. This has an important caveat: there are few female failures in the dataset and so the results may reflect that.
<- glue("{xlsx_prefix}/DE_Sex/t_sex_cure_table-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "male_vs_female") t_sex_table
## [1] 13971 68
<- glue("{xlsx_prefix}/DE_Sex/t_sex_cure_sig-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "male_vs_female")
t_sex_up_sig <- sig_reader(input_xlsx, "male_vs_female", "down") t_sex_down_sig
<- simple_gprofiler(
t_sex_up_gp
t_sex_up_sig,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/sex_male_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_sex_up_gp
## Error in eval(expr, envir, enclos): object 't_sex_up_gp' not found
::dotplot(t_sex_up_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_sex_up_gp' not found
::dotplot(t_sex_up_gp[["REAC_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_sex_up_gp' not found
::dotplot(t_sex_up_gp[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_sex_up_gp' not found
<- simple_gprofiler(
t_sex_down_gp
t_sex_down_sig,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/sex_female_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_sex_down_gp
## Error in eval(expr, envir, enclos): object 't_sex_down_gp' not found
Given the results from gProfiler, I do not have high expectations for clusterProfiler, so I am not likely to take the time to write them out. It seems like male/female is confounded with cure/fail.
<- simple_clusterprofiler(
t_sex_up_cp de_table = t_sex_table,
t_sex_up_sig, orgdb = "org.Hs.eg.db", kegg_prefix = "hs", do_kegg = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
::dotplot(t_sex_up_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- simple_clusterprofiler(
t_sex_down_cp de_table = t_sex_table,
t_sex_down_sig, orgdb = "org.Hs.eg.db", kegg_prefix = "hs", do_kegg = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
::dotplot(t_sex_down_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_sex_up_cp)
t_sex_topn_gsea "GO"]][[1]] t_sex_topn_gsea[[
Once again, the relevant files to load:
<- glue("{xlsx_prefix}/DE_Ethnicity/t_ethnicity_table-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "mestizo_indigenous") t_ethnicity_mestizo_indigenous
## [1] 14156 68
<- table_reader(input_xlsx, "mestizo_afrocol") t_ethnicity_mestizo_afrocol
## [1] 14156 68
<- table_reader(input_xlsx, "indigenous_afrocol") t_ethnicity_indigenous_afrocol
## [1] 14156 68
<- glue("{xlsx_prefix}/DE_Ethnicity/t_ethnicity_sig-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "mestizo_indigenous")
t_ethnicity_mestizo_indigenous_up <- sig_reader(input_xlsx, "mestizo_indigenous", "down")
t_ethnicity_mestizo_indigenous_down <- sig_reader(input_xlsx, "mestizo_afrocol")
t_ethnicity_mestizo_afrocol_up <- sig_reader(input_xlsx, "mestizo_afrocol", "down")
t_ethnicity_mestizo_afrocol_down <- sig_reader(input_xlsx, "indigenous_afrocol")
t_ethnicity_indigenous_afrocol_up <- sig_reader(input_xlsx, "indigenous_afrocol", "down") t_ethnicity_indigenous_afrocol_down
<- simple_gprofiler(
mestizo_indigenous_up_gp
t_ethnicity_mestizo_indigenous_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/ethnicity_mi_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
mestizo_indigenous_up_gp
## Error in eval(expr, envir, enclos): object 'mestizo_indigenous_up_gp' not found
<- simple_gprofiler(
indigenous_mestizo_up_gp
t_ethnicity_mestizo_indigenous_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/ethnicity_im_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
indigenous_mestizo_up_gp
## Error in eval(expr, envir, enclos): object 'indigenous_mestizo_up_gp' not found
<- simple_gprofiler(
mestizo_afrocol_up_gp
t_ethnicity_mestizo_afrocol_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/ethnicity_ma_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
mestizo_afrocol_up_gp
## Error in eval(expr, envir, enclos): object 'mestizo_afrocol_up_gp' not found
<- simple_gprofiler(
afrocol_mestizo_up_gp
t_ethnicity_mestizo_afrocol_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/ethnicity_am_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
afrocol_mestizo_up_gp
## Error in eval(expr, envir, enclos): object 'afrocol_mestizo_up_gp' not found
<- simple_gprofiler(
indigenous_afrocol_up_gp
t_ethnicity_indigenous_afrocol_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/ethnicity_ia_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
indigenous_afrocol_up_gp
## Error in eval(expr, envir, enclos): object 'indigenous_afrocol_up_gp' not found
<- simple_gprofiler(
afrocol_indigenous_up_gp
t_ethnicity_indigenous_afrocol_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/ethnicity_ai_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
afrocol_indigenous_up_gp
## Error in eval(expr, envir, enclos): object 'afrocol_indigenous_up_gp' not found
<- simple_clusterprofiler(
mestizo_indigenous_up_cp
t_ethnicity_mestizo_indigenous_up,de_table = t_ethnicity_mestizo_indigenous)
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
mestizo_indigenous_up_cp
## A set of ontologies produced by clusterprofiler.
<- simple_clusterprofiler(
indigenous_mestizo_up_cp t_ethnicity_mestizo_indigenous_down)
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
indigenous_mestizo_up_cp
## A set of ontologies produced by clusterprofiler.
<- simple_clusterprofiler(
mestizo_afrocol_up_cp
t_ethnicity_mestizo_afrocol_up,de_table = t_ethnicity_mestizo_afrocol)
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
mestizo_afrocol_up_cp
## A set of ontologies produced by clusterprofiler.
<- simple_clusterprofiler(t_ethnicity_mestizo_afrocol_down) afrocol_mestizo_up_cp
## Unable to find the fold-change column in the de table, not doing gsea.
afrocol_mestizo_up_cp
## A set of ontologies produced by clusterprofiler.
<- simple_clusterprofiler(
indigenous_afrocol_up_cp
t_ethnicity_indigenous_afrocol_up,de_table = t_ethnicity_indigenous_afrocol)
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
indigenous_afrocol_up_cp
## A set of ontologies produced by clusterprofiler.
<- simple_clusterprofiler(t_ethnicity_indigenous_afrocol_down) afrocol_indigenous_up_cp
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
afrocol_indigenous_up_cp
## A set of ontologies produced by clusterprofiler.
It looks like there are very few groups in the visit 1 significant genes.
The relevant xlsx files are:
<- glue("{cf_prefix}/Visits/t_clinical_v1_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx) t_cf_clinical_v1_table_sva
## [1] 14023 68
<- glue("{cf_prefix}/Visits/t_clinical_v1_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome")
t_cf_clinical_v1_sig_sva_up <- sig_reader(input_xlsx, "outcome", "down") t_cf_clinical_v1_sig_sva_down
<- simple_gprofiler(t_cf_clinical_v1_sig_sva_up) t_cf_clinical_v1_sig_sva_up_gp
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinical_v1_sig_sva_up_gp
## Error in eval(expr, envir, enclos): object 't_cf_clinical_v1_sig_sva_up_gp' not found
<- simple_gprofiler(t_cf_clinical_v1_sig_sva_down) t_cf_clinical_v1_sig_sva_down_gp
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_clinical_v1_sig_sva_down_gp
## Error in eval(expr, envir, enclos): object 't_cf_clinical_v1_sig_sva_down_gp' not found
::dotplot(t_cf_clinical_v1_sig_sva_down_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_clinical_v1_sig_sva_down_gp' not found
<- simple_cprofiler(
t_cf_clinical_v1_sig_sva_up_cp
t_cf_clinical_v1_sig_sva_up,de_table = t_cf_clinical_v1_table_sva,
orgdb = "org.Hs.eg.db")
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
t_cf_clinical_v1_sig_sva_up_cp
## A set of ontologies produced by clusterprofiler.
::dotplot(t_cf_clinical_v1_sig_sva_up_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- simple_cprofiler(
t_cf_clinical_v1_sig_sva_down_cp
t_cf_clinical_v1_sig_sva_down,orgdb = "org.Hs.eg.db")
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
It appears there are too few results to perform the gsea plots.
The relevant xlsx output may be found at:
<- glue("{cf_prefix}/Biopsies/t_biopsy_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_biopsy_table_sva
## [1] 13513 68
<- glue("{cf_prefix}/Biopsies/t_cf_biopsy_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome") t_cf_biopsy_sig_sva_up
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- sig_reader(input_xlsx, "outcome", "down") t_cf_biopsy_sig_sva_down
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- rbind.data.frame(t_cf_biopsy_sig_sva_up,
t_cf_biopsy_sig_sva_both t_cf_biopsy_sig_sva_down)
We only have 17 genes in the biopsies, but perhaps they are still interesting?
<- simple_gprofiler(
t_cf_biopsy_sig_sva_gp_up
t_cf_biopsy_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_biopsy_sig_sva_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_biopsy_sig_sva_gp_up
## Error in eval(expr, envir, enclos): object 't_cf_biopsy_sig_sva_gp_up' not found
::dotplot(t_cf_biopsy_sig_sva_gp_up[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_biopsy_sig_sva_gp_up' not found
<- enrichplot::pairwise_termsim(t_cf_biopsy_sig_sva_gp_up[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_biopsy_sig_sva_gp_up' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_biopsy_up_gp_go-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
<- simple_gprofiler(
t_cf_biopsy_sig_sva_gp_down
t_cf_biopsy_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_biopsy_sig_sva_down_gp-v{ver}.xlsx"))
t_cf_biopsy_sig_sva_gp_down
## A set of ontologies produced by gprofiler using 11
## genes against the hsapiens annotations and significance cutoff 0.05.
## There are:
## 0 MF
## 0 BP
## 0 KEGG
## 0 REAC
## 0 WP
## 0 TF
## 0 MIRNA
## 0 HPA
## 0 CORUM
## 0 HP hits.
## Not nearly as interesting
Again, clusterprofiler version
<- simple_cprofiler(
t_cf_biopsy_sig_sva_cp_up de_table = t_cf_biopsy_table_sva,
t_cf_biopsy_sig_sva_up, orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_biopsy_sig_sva_up_cp-v{ver}.xlsx"))
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_biopsy_sig_sva_cp_up[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_biopsy_sig_sva_cp_up)
t_cf_biopsy_sig_topn_gsea "GO_outcome_up"]][[1]] t_cf_biopsy_sig_topn_gsea[[
## NULL
<- glue("{cf_prefix}/Eosinophils/t_eosinophil_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_eosinophil_table_sva
## [1] 10532 68
<- glue("{cf_prefix}/Eosinophils/t_eosinophil_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome")
t_cf_eosinophil_sig_sva_up <- sig_reader(input_xlsx, "outcome", "down")
t_cf_eosinophil_sig_sva_down <- rbind.data.frame(t_cf_eosinophil_sig_sva_up,
t_cf_eosinophil_sig_sva_both t_cf_eosinophil_sig_sva_down)
<- simple_gprofiler(
t_cf_eosinophil_sig_sva_up_gp
t_cf_eosinophil_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_eosinophil_sig_sva_up_gp
## Error in eval(expr, envir, enclos): object 't_cf_eosinophil_sig_sva_up_gp' not found
::dotplot(t_cf_eosinophil_sig_sva_up_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_eosinophil_sig_sva_up_gp' not found
::dotplot(t_cf_eosinophil_sig_sva_up_gp[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_eosinophil_sig_sva_up_gp' not found
<- enrichplot::pairwise_termsim(t_cf_eosinophil_sig_sva_up_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_eosinophil_sig_sva_up_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "figures/t_cf_eosinophil_up_gp_go.svg",
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
<- enrichplot::pairwise_termsim(t_cf_eosinophil_sig_sva_up_gp[["REAC_enrich"]]) reac_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_eosinophil_sig_sva_up_gp' not found
<- sm(treeplot(reac_termsim, label_format = wrap_width)) reac_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'reac_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_eosinophil_up_gp_reac-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
reac_treeplot
## Error in eval(expr, envir, enclos): object 'reac_treeplot' not found
dev.off()
## png
## 2
<- simple_gprofiler(
t_cf_eosinophil_sig_sva_down_gp
t_cf_eosinophil_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
::dotplot(t_cf_eosinophil_sig_sva_down_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_eosinophil_sig_sva_down_gp' not found
<- enrichplot::pairwise_termsim(t_cf_eosinophil_sig_sva_down_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_eosinophil_sig_sva_down_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_eosinophil_down_gp_go-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
## There is only one reactome hit, so not plotting it.
I evaluated this and the ‘up’ set next to each other and they are extremely similar:
up: 148 GO hits, 68 TF, 0 HPA both: 169 GO, 69 TF, and 2 HPA
Otherwise I think they are the same.
<- simple_gprofiler(
t_cf_eosinophil_sig_sva_both_gp
t_cf_eosinophil_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_both_gp-v{ver}.xlsx"))
## Error in function (type, msg, asError = TRUE) : Recv failure: Connection reset by peer
t_cf_eosinophil_sig_sva_both_gp
## Error in eval(expr, envir, enclos): object 't_cf_eosinophil_sig_sva_both_gp' not found
::dotplot(t_cf_eosinophil_sig_sva_both_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_eosinophil_sig_sva_both_gp' not found
<- enrichplot::pairwise_termsim(t_cf_eosinophil_sig_sva_both_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_eosinophil_sig_sva_both_gp' not found
<- sm(treeplot(go_termsim, label_formap = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_eosinophil_both_gp_go-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
<- enrichplot::pairwise_termsim(t_cf_eosinophil_sig_sva_both_gp[["REAC_enrich"]]) reac_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_eosinophil_sig_sva_both_gp' not found
<- sm(treeplot(reac_termsim, label_format = wrap_width)) reac_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'reac_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_eosinophil_both_gp_reac-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
reac_treeplot
## Error in eval(expr, envir, enclos): object 'reac_treeplot' not found
dev.off()
## png
## 2
<- simple_cprofiler(
t_cf_eosinophil_sig_sva_cp_up de_table = t_cf_eosinophil_table_sva,
t_cf_eosinophil_sig_sva_up, orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_sig_sva_up_cp-v{ver}.xlsx"))
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_eosinophil_sig_sva_cp_up[["enrich_objects"]][["BP_all"]]) enrichplot
<- simple_cprofiler(
t_cf_eosinophil_sig_sva_cp_down
t_cf_eosinophil_sig_sva_down,orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_sig_sva_down_cp-v{ver}.xlsx"))
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_eosinophil_sig_sva_cp_down[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_eosinophil_sig_sva_cp_up)
t_cf_eosinophil_sig_topn_gsea "GO_outcome_up"]][[1]] t_cf_eosinophil_sig_topn_gsea[[
## NULL
<- glue("{cf_prefix}/Monocytes/t_monocyte_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_monocyte_table_sva
## [1] 10862 68
<- glue("{cf_prefix}/Monocytes/t_monocyte_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome")
t_cf_monocyte_sig_sva_up <- sig_reader(input_xlsx, "outcome", "down")
t_cf_monocyte_sig_sva_down <- rbind.data.frame(t_cf_monocyte_sig_sva_up,
t_cf_monocyte_sig_sva_both t_cf_monocyte_sig_sva_down)
Now that I am looking back over these results, I am not compeltely certain why I only did the gprofiler search for the sva data…
<- simple_gprofiler(
t_cf_monocyte_sig_sva_up_gp
t_cf_monocyte_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_monocyte_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_monocyte_sig_sva_up_gp
## Error in eval(expr, envir, enclos): object 't_cf_monocyte_sig_sva_up_gp' not found
::dotplot(t_cf_monocyte_sig_sva_up_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_monocyte_sig_sva_up_gp' not found
::dotplot(t_cf_monocyte_sig_sva_up_gp[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_monocyte_sig_sva_up_gp' not found
<- enrichplot::pairwise_termsim(t_cf_monocyte_sig_sva_up_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_monocyte_sig_sva_up_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "figures/overrepresentation/t_cf_monocyte_up_gp_go.svg",
height = treeplot_height, width = treeplot_width)
## Warning in pp(file = "figures/overrepresentation/t_cf_monocyte_up_gp_go.svg", :
## The directory: figures/overrepresentation does not exist, will attempt to
## create it.
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
<- simple_gprofiler(
t_cf_monocyte_sig_sva_down_gp
t_cf_monocyte_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_monocyte_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
::dotplot(t_cf_monocyte_sig_sva_down_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_monocyte_sig_sva_down_gp' not found
<- enrichplot::pairwise_termsim(t_cf_monocyte_sig_sva_down_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_monocyte_sig_sva_down_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_monocyte_down_gp_go-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
## Insufficient results to make a tree plot.
<- simple_gprofiler(
t_cf_monocyte_sig_sva_both_gp
t_cf_monocyte_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_monocyte_both_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_monocyte_sig_sva_both_gp
## Error in eval(expr, envir, enclos): object 't_cf_monocyte_sig_sva_both_gp' not found
::dotplot(t_cf_monocyte_sig_sva_both_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_monocyte_sig_sva_both_gp' not found
<- enrichplot::pairwise_termsim(t_cf_monocyte_sig_sva_both_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_monocyte_sig_sva_both_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_monocyte_both_gp_go-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
## Insufficient results for reactome
<- enrichplot::pairwise_termsim(t_cf_monocyte_sig_sva_both_gp[["TF_enrich"]]) tf_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_monocyte_sig_sva_both_gp' not found
<- sm(treeplot(tf_termsim, label_format = wrap_width)) tf_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'tf_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_monocyte_both_gp_tf-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
tf_treeplot
## Error in eval(expr, envir, enclos): object 'tf_treeplot' not found
dev.off()
## png
## 2
tf_treeplot
## Error in eval(expr, envir, enclos): object 'tf_treeplot' not found
<- simple_cprofiler(
t_cf_monocyte_sig_sva_cp_up de_table = t_cf_monocyte_table_sva,
t_cf_monocyte_sig_sva_up, orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_monocyte_sig_sva_up_cp-v{ver}.xlsx"))
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_monocyte_sig_sva_cp_up[["enrich_objects"]][["BP_all"]]) enrichplot
<- simple_cprofiler(
t_cf_monocyte_sig_sva_cp_down
t_cf_monocyte_sig_sva_down,orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_monocyte_sig_sva_down_cp-v{ver}.xlsx"))
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_monocyte_sig_sva_cp_down[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_monocyte_sig_sva_cp_up)
t_cf_monocyte_sig_topn_gsea "GO_outcome_up"]][[1]] t_cf_monocyte_sig_topn_gsea[[
## NULL
<- glue("{cf_prefix}/Neutrophils/t_neutrophil_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_neutrophil_table_sva
## [1] 9101 68
<- glue("{cf_prefix}/Neutrophils/t_neutrophil_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome")
t_cf_neutrophil_sig_sva_up <- sig_reader(input_xlsx, "outcome", "down")
t_cf_neutrophil_sig_sva_down <- rbind.data.frame(t_cf_neutrophil_sig_sva_up,
t_cf_neutrophil_sig_sva_both t_cf_neutrophil_sig_sva_down)
Now that I am looking back over these results, I am not compeltely certain why I only did the gprofiler search for the sva data…
<- simple_gprofiler(
t_cf_neutrophil_sig_sva_up_gp
t_cf_neutrophil_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_up_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_neutrophil_sig_sva_up_gp
## Error in eval(expr, envir, enclos): object 't_cf_neutrophil_sig_sva_up_gp' not found
::dotplot(t_cf_neutrophil_sig_sva_up_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_neutrophil_sig_sva_up_gp' not found
::dotplot(t_cf_neutrophil_sig_sva_up_gp[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_neutrophil_sig_sva_up_gp' not found
<- enrichplot::pairwise_termsim(t_cf_neutrophil_sig_sva_up_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_neutrophil_sig_sva_up_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = "figures/t_cf_neutrophil_up_gp_go.svg",
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
<- simple_gprofiler(
t_cf_neutrophil_sig_sva_down_gp
t_cf_neutrophil_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_neutrophil_sig_sva_down_gp
## Error in eval(expr, envir, enclos): object 't_cf_neutrophil_sig_sva_down_gp' not found
## Not much to work with here.
<- simple_gprofiler(
t_cf_neutrophil_sig_sva_both_gp
t_cf_neutrophil_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_both_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_neutrophil_sig_sva_both_gp
## Error in eval(expr, envir, enclos): object 't_cf_neutrophil_sig_sva_both_gp' not found
::dotplot(t_cf_neutrophil_sig_sva_both_gp[["BP_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_neutrophil_sig_sva_both_gp' not found
::dotplot(t_cf_neutrophil_sig_sva_both_gp[["TF_enrich"]]) enrichplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'dotplot': object 't_cf_neutrophil_sig_sva_both_gp' not found
<- enrichplot::pairwise_termsim(t_cf_neutrophil_sig_sva_both_gp[["BP_enrich"]]) go_termsim
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'pairwise_termsim': object 't_cf_neutrophil_sig_sva_both_gp' not found
<- sm(treeplot(go_termsim, label_format = wrap_width)) go_treeplot
## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'treeplot': object 'go_termsim' not found
pp(file = glue("images/overrepresentation/t_cf_neutrophil_both_gp_go-v{ver}.pdf"),
height = treeplot_height, width = treeplot_width)
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
dev.off()
## png
## 2
go_treeplot
## Error in eval(expr, envir, enclos): object 'go_treeplot' not found
## Insufficient results for reactome
<- simple_cprofiler(
t_cf_neutrophil_sig_sva_cp_up de_table = t_cf_neutrophil_table_sva,
t_cf_neutrophil_sig_sva_up, orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_sig_sva_up_cp-v{ver}.xlsx"))
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the BP data.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Finished writing excel file.
::dotplot(t_cf_neutrophil_sig_sva_cp_up[["enrich_objects"]][["BP_all"]]) enrichplot
<- simple_cprofiler(
t_cf_neutrophil_sig_sva_cp_down
t_cf_neutrophil_sig_sva_down,orgdb = "org.Hs.eg.db",
excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_sig_sva_down_cp-v{ver}.xlsx"))
## Unable to find the fold-change column in the de table, not doing gsea.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Writing a sheet containing the legend.
##
## Writing the MF data.
##
## Writing the CC data.
##
## Writing the KEGG data.
##
## Finished writing excel file.
::dotplot(t_cf_neutrophil_sig_sva_cp_down[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_neutrophil_sig_sva_cp_up)
t_cf_neutrophil_sig_topn_gsea "GO_outcome_up"]][[1]] t_cf_neutrophil_sig_topn_gsea[[
## NULL
<- glue("{cf_prefix}/Monocytes/t_monocyte_v1_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_monocyte_v1_table_sva
## [1] 10482 68
<- glue("{cf_prefix}/Monocytes/t_monocyte_v1_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome") t_cf_monocyte_v1_sig_sva_up
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- sig_reader(input_xlsx, "outcome", "down")
t_cf_monocyte_v1_sig_sva_down <- rbind.data.frame(t_cf_monocyte_v1_sig_sva_up,
t_cf_monocyte_v1_sig_sva_both t_cf_monocyte_v1_sig_sva_down)
V1: Up: 14 genes; No categories V1: Down: 52 genes; 20 GO, 5 TF
<- simple_gprofiler(
t_cf_monocyte_v1_sig_sva_up_gp
t_cf_monocyte_v1_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_up_gp-v{ver}.xlsx"))
t_cf_monocyte_v1_sig_sva_up_gp
## A set of ontologies produced by gprofiler using 14
## genes against the hsapiens annotations and significance cutoff 0.05.
## There are:
## 0 MF
## 0 BP
## 0 KEGG
## 0 REAC
## 0 WP
## 0 TF
## 0 MIRNA
## 0 HPA
## 0 CORUM
## 0 HP hits.
<- simple_gprofiler(
t_cf_monocyte_v1_sig_sva_down_gp
t_cf_monocyte_v1_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_monocyte_v1_sig_sva_down_gp
## Error in eval(expr, envir, enclos): object 't_cf_monocyte_v1_sig_sva_down_gp' not found
<- simple_gprofiler(
t_cf_monocyte_v1_sig_sva_both_gp
t_cf_monocyte_v1_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_monocyte_v1_sig_sva_both_gp
## Error in eval(expr, envir, enclos): object 't_cf_monocyte_v1_sig_sva_both_gp' not found
I like cats!
<- simple_cprofiler(t_cf_monocyte_v1_sig_sva_up,
t_cf_monocyte_v1_sig_sva_up_cp
t_cf_monocyte_v1_table_sva,orgdb = "org.Hs.eg.db")
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
::dotplot(t_cf_monocyte_v1_sig_sva_up_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_monocyte_v1_sig_sva_up_cp)
t_cf_monocyte_v1_topn_gsea "GO_outcome_up"]][[1]] t_cf_monocyte_v1_topn_gsea[[
## NULL
<- glue("{cf_prefix}/Neutrophils/t_neutrophil_v1_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_neutrophil_v1_table_sva
## [1] 8717 68
<- glue("{cf_prefix}/Neutrophils/t_neutrophil_v1_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome") t_cf_neutrophil_v1_sig_sva_up
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- sig_reader(input_xlsx, "outcome", "down") t_cf_neutrophil_v1_sig_sva_down
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- rbind.data.frame(t_cf_neutrophil_v1_sig_sva_up,
t_cf_neutrophil_v1_sig_sva_both t_cf_neutrophil_v1_sig_sva_down)
<- simple_gprofiler(
t_cf_neutrophil_v1_sig_sva_up_gp
t_cf_neutrophil_v1_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_up_gp-v{ver}.xlsx"))
## There are only, 5 returning null.
t_cf_neutrophil_v1_sig_sva_up_gp
## NULL
<- simple_gprofiler(
t_cf_neutrophil_v1_sig_sva_down_gp
t_cf_neutrophil_v1_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_down_gp-v{ver}.xlsx"))
## There are only, 8 returning null.
t_cf_neutrophil_v1_sig_sva_down_gp
## NULL
<- simple_gprofiler(
t_cf_neutrophil_v1_sig_sva_both_gp
t_cf_neutrophil_v1_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_neutrophil_down_gp-v{ver}.xlsx"))
t_cf_neutrophil_v1_sig_sva_both_gp
## A set of ontologies produced by gprofiler using 13
## genes against the hsapiens annotations and significance cutoff 0.05.
## There are:
## 0 MF
## 0 BP
## 0 KEGG
## 0 REAC
## 0 WP
## 0 TF
## 0 MIRNA
## 0 HPA
## 0 CORUM
## 0 HP hits.
<- simple_cprofiler(t_cf_neutrophil_v1_sig_sva_up,
t_cf_neutrophil_v1_sig_sva_up_cp
t_cf_neutrophil_v1_table_sva,orgdb = "org.Hs.eg.db")
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
## Scale for size is already present.
## Adding another scale for size, which will replace the existing scale.
::dotplot(t_cf_neutrophil_v1_sig_sva_up_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_neutrophil_v1_sig_sva_up_cp)
t_cf_neutrophil_v1_topn_gsea "GO_outcome_up"]][[1]] t_cf_neutrophil_v1_topn_gsea[[
## NULL
<- glue("{cf_prefix}/Eosinophils/t_eosinophil_v1_cf_table_sva-v{ver}.xlsx")
input_xlsx <- table_reader(input_xlsx, "outcome") t_cf_eosinophil_v1_table_sva
## [1] 9979 68
<- glue("{cf_prefix}/Eosinophils/t_eosinophil_v1_cf_sig_sva-v{ver}.xlsx")
input_xlsx <- sig_reader(input_xlsx, "outcome") t_cf_eosinophil_v1_sig_sva_up
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- sig_reader(input_xlsx, "outcome", "down") t_cf_eosinophil_v1_sig_sva_down
## There are less than 20 rows in this significance table, it is unlikely to be interesting.
<- rbind.data.frame(t_cf_eosinophil_v1_sig_sva_up,
t_cf_eosinophil_v1_sig_sva_both t_cf_eosinophil_v1_sig_sva_down)
<- simple_gprofiler(
t_cf_eosinophil_v1_sig_sva_up_gp
t_cf_eosinophil_v1_sig_sva_up,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_up_gp-v{ver}.xlsx"))
t_cf_eosinophil_v1_sig_sva_up_gp
## A set of ontologies produced by gprofiler using 13
## genes against the hsapiens annotations and significance cutoff 0.05.
## There are:
## 0 MF
## 0 BP
## 0 KEGG
## 0 REAC
## 0 WP
## 0 TF
## 0 MIRNA
## 0 HPA
## 0 CORUM
## 0 HP hits.
<- simple_gprofiler(
t_cf_eosinophil_v1_sig_sva_down_gp
t_cf_eosinophil_v1_sig_sva_down,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_eosinophil_v1_sig_sva_down_gp
## Error in eval(expr, envir, enclos): object 't_cf_eosinophil_v1_sig_sva_down_gp' not found
<- simple_gprofiler(
t_cf_eosinophil_v1_sig_sva_both_gp
t_cf_eosinophil_v1_sig_sva_both,excel = glue("{xlsx_prefix}/Gene_Set_Enrichment/t_cf_eosinophil_down_gp-v{ver}.xlsx"))
## Error in gprofiler_request(url, body): There's an issue with your request to g:Profiler.
## Error code: 503.
## Please double check your input. If this doesn't help, then check your internet connection or contact us with a reproducible example on biit.support@ut.ee
t_cf_eosinophil_v1_sig_sva_both_gp
## Error in eval(expr, envir, enclos): object 't_cf_eosinophil_v1_sig_sva_both_gp' not found
<- simple_cprofiler(t_cf_eosinophil_v1_sig_sva_up,
t_cf_eosinophil_v1_sig_sva_up_cp
t_cf_eosinophil_v1_table_sva,orgdb = "org.Hs.eg.db")
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
::dotplot(t_cf_eosinophil_v1_sig_sva_up_cp[["enrich_objects"]][["BP_all"]]) enrichplot
<- plot_topn_gsea(t_cf_eosinophil_v1_sig_sva_up_cp)
t_cf_eosinophil_v1_topn_gsea "GO_outcome_up"]][[1]] t_cf_eosinophil_v1_topn_gsea[[
## NULL