plot_multi | R Documentation |
Visualize multiple PSI or cRPKM values in a single plot.
plot_multi(df, config = NULL, subg = FALSE, expr = FALSE, trim_colnames = FALSE, qual = c("VLOW", "N", "LOW", "OK", "SOK"), counts = FALSE, xlab = "", ylab = "", title = "", cluster_rows = TRUE, cluster_cols = ifelse(is.null(config), TRUE, FALSE), fill = NULL, usepkg = c("ggplot2", "gplots", "pheatmap"), ...)
df |
A data frame of input values (PSI or cRPKM). If the latter, need to
set |
config |
Optional configuration settings. Can be
a path to the |
subg |
Logical indicating whether samples should be subgrouped for plotting. |
expr |
Logical - |
trim_colnames |
String that must be searched for and trimmed at the end
of every sample column in x. Useful to trim the "-cRPKM" suffix from expression
tables. If no string must be trimmed, leave as |
qual |
String indicating the minimun vast-tools quality score
for the PSI to be accepted. Defaults to |
counts |
Logical indicating whether the data frame contains read counts.
Set to |
xlab |
The x-axis label |
ylab |
The y-axis label |
title |
Title of the plot |
cluster_rows |
Logical to cluster rows using hierarchical clustering |
cluster_cols |
Logical to cluster columns using hierarchical clustering |
fill |
A vector of colours. e.g. from |
usepkg |
Default is |
... |
Additional parameters passed to |
By default, geom_tile
is used to generate a heatmap
and a ggplot2
object is returned. Alternatively, other heatmap
packages are supported including: pheatmap
(use usepkgs = "pheatmap"
) and
heatmap.2
(use usepkgs = "gplots"
).
Input is similar to plot_event
, plot_expr
, or
plot_multievent
. Subgrouping of samples is also supported (see
plot_event
and preprocess_sample_colors
for details
on subgrouping). If subgroups are activated, the PSI for each subgroup is taken
as the average of all the samples in the subgroup.
If cluster_rows = TRUE
, then a hierarchical clustering using hclust
will be performed on a distance matrix computed by dist
. If config
is not specified, then the samples will also be clustered.
To set the colours, use fill
option to specify vector of colours.
By default (fill=NULL
), PSI uses a yellow/blue gradient, while cRPKMs
uses the "YlOrRd" color brewer palette.
# Uses ggplot2 by default plot_multi(psi) plot_multi(psi, config = config) # Use expr = TRUE for cRPKMs plot_multi(crpkm, expr = TRUE) plot_multi(crpkm, config = config, expr = TRUE) plot_multi(crpkm, config = config, expr = TRUE, cluster_rows = TRUE) # To use pheatmap or gplots for plotting, set usepgk option plot_multi(psi, config = config, usepkg = "pheatmap") # To enable sample subgroups, set subg = TRUE plot_multi(psi, config = config, subg = TRUE) # Working with expression tables with read counts and suffixes, enabling subgroups plot_multi(crpkm_counts, config = config, expr = TRUE, trim_colnames = "-cRPKM", counts = TRUE)
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