8 jjVolcano

jjVolcano function can be used to visualize marker genes in multiple clusters.

8.1 Basic examples

Load test data:

library(scRNAtoolVis)

# test
data('pbmc.markers')

# check
head(pbmc.markers,3)
#               p_val avg_log2FC pct.1 pct.2     p_val_adj     cluster  gene
# RPS12 2.008629e-140  0.7256738 1.000 0.991 2.754633e-136 Naive CD4 T RPS12
# RPS27 2.624075e-140  0.7242847 0.999 0.992 3.598656e-136 Naive CD4 T RPS27
# RPS6  1.280169e-138  0.6742630 1.000 0.995 1.755623e-134 Naive CD4 T  RPS6

plot:

# plot
jjVolcano(diffData = pbmc.markers)

Ajustlog2FC.cutoff,col.typeandtopGeneN:

# change aes color type
jjVolcano(diffData = pbmc.markers,
          log2FC.cutoff = 0.5,
          col.type = "adjustP",
          topGeneN = 3)

Supply with own genes:

# supply own genes
mygene <- c('LTB','CD79B','CCR7','GNLY')

jjVolcano(diffData = pbmc.markers,
          myMarkers = mygene)

Change point color:

# change point color
jjVolcano(diffData = pbmc.markers,
          aesCol = c('purple','orange'))

Change rect fill color:

# change cluster rect color
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdBu', 15)[4:12])

Other about gene text aruments can be passed by geom_text_repel:

# cluster label arguments passed to geom_text_repel
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdBu', 15)[4:12],
          size  = 3.5,
          fontface = 'italic')

Ajust cluster orders by cluster.order:

# ajust cluster orders
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('PuOr', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          cluster.order = rev(unique(pbmc.markers$cluster)))

8.2 Layout

flip = T to rotate the plot:

# flip the plot
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('PiYG', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          legend.position = c(0.8,0.2),
          flip = T)

polar = T to draw a polar plot:

# make a polar plot
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdBu', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          polar = T)

Expand the limits:

# expand limits
jjVolcano(diffData = pbmc.markers,
          tile.col = corrplot::COL2('RdYlBu', 15)[4:12],
          size  = 3.5,
          fontface = 'italic',
          polar = T) +
  ylim(-8,10)

7 jjDotPlot