Grioni, Andrea 2021-06-09
devtools::install_github("andreagrioni/ToolViz")
library(ToolViz)
#> Warning: replacing previous import 'dplyr::collapse' by 'glue::collapse' when
#> loading 'ToolViz'
data("test_data")
The function is adapted from Cédric Scherer’s blog here
Function arguments:
The annotation must have a column named SeqId
with ProbeIds as values
and a column named EntrezGeneSymbol
with the corresponding gene name.
plot_raincloud(
test_data,
#annotation=anno_v4,
target='seq.10008.43',
x='Sample...Visit.Description..clin.event.',
group_ids = 'ARM',
spaghetti="Sample...Screening.ID",
colspaghetti='PlateId'
)
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
#ggsave("PATH/TO/FILE.png", dpi=300, width = 15, height=15)
Function arguments:
The annotation must have a column named SeqId
with ProbeIds as values
and a column named EntrezGeneSymbol
with the corresponding gene name.
ToolViz::plot_dist(
test_data,
#annotation=anno_v4,
target='seq.10008.43',
x='Sample...Visit.Description..clin.event.',
#rows_by="ARM",
cols_by='ARM',
kind="grid",
x_rot=45,
scales_grid='free_y',
spaghetti="Sample...Screening.ID",
colspaghetti='SEX',
stats=TRUE,
x_lab="time")
#> Warning: `fun.y` is deprecated. Use `fun` instead.
#ggsave("PATH/TO/FILE.png", dpi=300, width = 15, height=15)
Function useful to debug experiment where some of the samples were corrupted. The heatmap helps to identify if corrupted samples originated from a cluster/region of the plate.
The function looks for the column named PlatePosition
and separate it
into column_location
and row_location
.
Function arguments:
draw_heatmap(
table=test_data,
color_by="ARM",
text_by="SEX",
title="heatmap 96-well plate position",
text_size=4)
#ggsave("PATH/TO/FILE.png", dpi=300, width = 15, height=15)
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