In lea-rothoerl/DeeDee: Comparative Evaluation and Visualization of Differential Expression Analyses

knitr::opts_chunk$set(echo = TRUE,
                      warning = FALSE,
                      message = FALSE,
                      error = TRUE)

About this document

This document contains the results of running all main DeeDee functions on your provided input data and parameters.

Your contrasts:

names(deedee_list)

library(DeeDee)

DeeDee scatter plot

  deedee_scatter(data = deedee_list,
                 pthresh = pthresh,
                 select1 = scatter_select1,
                 select2 = scatter_select2,
                 color_by = scatter_color_by)

Your parameters:

• pthresh = r pthresh
• select1 = r scatter_select1
• select2 = r scatter_select2
• color_by = r scatter_color_by

---

DeeDee heatmap

  deedee_heatmap(data = deedee_list,
                 pthresh = pthresh,
                 show_first = heatmap_show_first,
                 show_gene_names = heatmap_show_gene_names,
                 dist = heatmap_dist,
                 clust = heatmap_clust,
                 show_na = heatmap_show_na)

Your parameters:

• pthresh = r pthresh
• show_first = r heatmap_show_first
• show_gene_names = r heatmap_show_gene_names
• dist = r heatmap_dist
• clust = r heatmap_clust
• show_na = r heatmap_show_na

---

DeeDee Venn diagram

  deedee_venn(data = deedee_list,
              pthresh = pthresh,
              mode = venn_mode)

Your parameters:

• pthresh = r pthresh
• mode = r venn_mode

---

DeeDee UpSet plot

  deedee_upset(data = deedee_list,
               pthresh = pthresh,
               mode = upset_mode,
               min_setsize = upset_min_setsize)

Your parameters:

• pthresh = r pthresh
• mode = r upset_mode
• min_setsize = r upset_min_setsize

---

DeeDee Q-Q plot

  deedee_qqmult(data = deedee_list,
                pthresh = pthresh,
                ref = qqmult_ref)

Your parameters:

• pthresh = r pthresh
• ref = r qqmult_ref

---

DeeDee CAT plot

  deedee_cat(data = deedee_list,
             pthresh = pthresh,
             ref = cat_ref,
             maxrank = cat_maxrank,
             mode = cat_mode)

Your parameters:

• pthresh = r pthresh
• ref = r cat_ref
• maxrank = r cat_maxrank
• mode = r cat_mode

---

Session info {-}

sessionInfo()

lea-rothoerl/DeeDee documentation built on Dec. 21, 2021, 9:47 a.m.