Install RVA
install.packages("RVA")
Load package for use
library(RVA)
Let’s load a summary statistics tables and combine them into a list named d1.
<- RVA::Sample_summary_statistics_table
df <- RVA::Sample_summary_statistics_table1
df1 <- list(df, df1) d1
This is head of the first summary statictic table present in the list:
logFC | AveExpr | t | P.Value | adj.P.Val | B | |
---|---|---|---|---|---|---|
ENSG00000123610.5 | -1.2886593 | 4.306067 | -8.647905 | 0 | 0 | 28.14522 |
ENSG00000148926.10 | -0.9519794 | 6.083623 | -8.015885 | 0 | 0 | 23.54129 |
ENSG00000141664.9 | -0.8942611 | 5.356978 | -7.922250 | 0 | 0 | 22.86899 |
ENSG00000104320.13 | -0.5723190 | 4.574599 | -7.853658 | 0 | 0 | 22.36399 |
ENSG00000120217.14 | -1.2170891 | 3.112864 | -7.874408 | 0 | 0 | 22.31510 |
ENSG00000152778.9 | -0.9307776 | 4.302267 | -7.771144 | 0 | 0 | 21.76999 |
The row names are gene id, the supported gene id can be one of: ACCNUM, ALIAS, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, ENTREZID, ENZYME, EVIDENCE, EVIDENCEALL, GENENAME, GO, GOALL, IPI, MAP, OMIM. For the provided sample datasets in this package we only have ENSEMBL id’s for gene id type.
This function checks the number of differencialy expressed (DE) genes at different cutoff combinations. It process summary statistics table generated by differential expression analysis like limma or DESeq2, as input data, to evaluate the number of differntially expressed genes with different FDR and fold change cutoff.
Below are the default parameters for plot_cutoff. You can change them
to modify your output. Use help(plot_cutoff)
to learn more
about the parameters.
plot_cutoff(data = data,
comp.names = NULL,
FCflag = "logFC",
FDRflag = "adj.P.Val",
FCmin = 1.2,
FCmax = 2,
FCstep = 0.1,
p.min = 0,
p.max = 0.2,
p.step = 0.01,
plot.save.to = NULL,
gen.3d.plot = TRUE,
gen.plot = TRUE)
<- plot_cutoff(data = df,
cutoff.result gen.plot = TRUE,
gen.3d.plot = TRUE)
The result object cutoff.result takes a data frame as an input data and contains 3 objects:
1. A table that summarizes the number of DE genes under threshold combination
head(cutoff.result[[1]])
pvalue | FC | Number_of_Genes |
---|---|---|
0 | 1.2 | 0 |
0.01 | 1.2 | 1135 |
0.02 | 1.2 | 1246 |
0.03 | 1.2 | 1302 |
0.04 | 1.2 | 1345 |
0.05 | 1.2 | 1388 |
2. A 3D plotly object, where the x-axis is Fold change threshold, y-axis is FDR cutoff, and z-axis is the number of DE genes under the x,y combination:
2]] cutoff.result[[
3. A plot to visualize it:
3]] cutoff.result[[
Saving figures
Figures can be saved using two approaches:
1. Using imbedded fucntion with predetermined dpi
plot_cutoff(data = df,
plot.save.to = "cut_off_selection_plot.png")
2. Using ggsave from the ggplot2 library with option to customize the width, height and dpi.
library(ggplot2)
ggsave("cut_off_selection_plot.png", cutoff.result[[3]], width = 5, height = 5, dpi = 300)
<- plot_cutoff(data = d1,
cutoff.result.list comp.names = c('a', 'b'))
The result object cutoff.result.list takes a list as an input data and contains 2 objects:
1. A table that summarizes the number of DE genes under threshold combination for each of the data frames in the list.
head(cutoff.result.list[[1]])
Comparisons.ID | pvalue | FC | Number_of_Genes |
---|---|---|---|
a | 0.01 | 1.2 | 1135 |
a | 0.05 | 1.2 | 1388 |
a | 0.1 | 1.2 | 1526 |
a | 0.2 | 1.2 | 1712 |
a | 0.01 | 1.3 | 514 |
a | 0.05 | 1.3 | 606 |
2. A plot to visualize it. A 3D plotly object is not created for a list input data.
cutoff.result.list
Saving figures
Figures can be saved using two approaches:
1. Using imbedded fucntion with predetermined dpi
plot_cutoff(data = d1,
comp.names = c("A", "B"),
plot.save.to = "cut_off_list_plot.png")
2. Using ggsave from the ggplot2 library with option to customize the width, height and dpi.
library(ggplot2)
ggsave("cut_off_list_plot.png", cutoff.result.list, width = 5, height = 5, dpi = 300)
This is the function to generate a qqplot object with confidence interval from the input data. The input data is a summary statistics table or a list that contains multiple summary statistics tables from limma or DEseq2, where each row is a gene.
<- plot_qq(df)
qq.result qq.result
Saving figures
Figures can be saved using two approaches:
1. Using imbedded fucntion with predetermined dpi
plot_qq(data = df,
plot.save.to = "qq_plot.png")
2. Using ggsave from the ggplot2 library with option to customize the width, height and dpi.
library(ggplot2)
ggsave("qq_plot.png", qq.result, width = 5, height = 5, dpi = 300)
plot_qq function can also take a list as an input data, but requires comp.names to be specified. The result object is a set of qq plots for each of the data frames in the list.
<- plot_qq(data = d1,
qq.list.result comp.names = c('A', 'B'))
qq.list.result
Saving figures
Figures can be saved using two approaches:
1. Using imbedded fucntion with predetermined dpi
plot_qq(data = d1,
comp.names = c("A", "B"),
plot.save.to = "qq_list_plot.png")
2. Using ggsave from the ggplot2 library with option to customize the width, height and dpi.
library(ggplot2)
ggsave("qq_list_plot.png", qq.list.result, width = 5, height = 5, dpi = 300)
This is the function to process the summary statistics table generated by differential expression analysis like limma or DESeq2 and generate the volcano plot with the option of highlighting the individual genes or gene set of interest (like disease-related genes from Disease vs Healthy comparison). The input data is a summary statistics table or a list that contains multiple summary statistics tables from limma or DEseq2, where each row is a gene.
Below are the default parameters for plot_volcano. You can change
them to modify your output. Use help(plot_volcano)
to learn
more about the parameters.
plot_volcano(
data = data,
comp.names = NULL,
geneset = NULL,
geneset.FCflag = "logFC",
highlight.1 = NULL,
highlight.2 = NULL,
upcolor = "#FF0000",
downcolor = "#0000FF",
plot.save.to = NULL,
xlim = c(-4, 4),
ylim = c(0, 12),
FCflag = "logFC",
FDRflag = "adj.P.Val",
highlight.FC.cutoff = 1.5,
highlight.FDR.cutoff = 0.05,
title = "Volcano plot",
xlab = "log2 Fold Change",
ylab = "log10(FDR)"
)
plot_volcano(data = df)
Volcano Plot can also take a list as an input data with specified comp.name for each data frame.
plot_volcano(data = d1,
comp.names = c('a', 'b'))
You can highlight gene sets (like disease related genes from a Disease vs Healthy comparison).
The gene set to be highlighted in the volcano plot can be spesified in two ways:
1. A summary statistics table with the highlighted genes as row names (the gene name format needs to be consistent with the main summary statistics table). For example, this summary statistics table could be the statistical analysis output from a Disease vs Healthy comparison (only containing the subsetted significant genes).
2. One or two vectors consisting of gene names. The gene name format needs to be consistent with the main summary statistics table. It can be set by the parameters highlight.1 and highlight.2. For example, you can assign the up-regulated gene list from the Disease vs Healthy comparison to highlight.1 and down-regulated gene list from the comparison to highlight.2.
Example using option 1 (use summary statistics table’s row name to highlight genes):
#disease gene set used to color volcanoplot
<- RVA::Sample_disease_gene_set dgs
head(dgs)
logFC | AveExpr | t | P.Value | adj.P.Val | B | |
---|---|---|---|---|---|---|
ENSG00000176749.9 | 0.1061454 | 6.034635 | -1.1704309 | 0.2446236 | 0.9188735 | -5.6468338 |
ENSG00000086619.13 | 0.0862010 | 2.100165 | -0.3331558 | 0.7397177 | 0.9989991 | -5.7218518 |
ENSG00000198324.13 | -0.1321791 | 5.702730 | 1.2768794 | 0.2046170 | 0.8889442 | -5.5265238 |
ENSG00000134531.10 | -0.4778738 | 4.562272 | 3.6721593 | 0.0003892 | 0.0298096 | -0.1135281 |
ENSG00000116260.17 | 0.1842322 | 2.905702 | 1.6108394 | 0.1103830 | 0.7809130 | -4.7560495 |
ENSG00000104518.11 | 0.1452149 | -3.776628 | 0.2584838 | 0.7965675 | 0.9989991 | -4.9101962 |
You can also specify the range of the plot by xlim and ylim.
plot_volcano(data = df,
geneset = dgs,
upcolor = "#FF0000",
downcolor = "#0000FF",
xlim = c(-3,3),
ylim = c(0,14))
By default, the genes which have positive fold change in the provided geneset parameter will be colored yellow, and negative fold will be colored purple, this also can be changed by specifying upcolor and downcolor:
plot_volcano(data = d1,
comp.names = c('a', 'b'),
geneset = dgs,
upcolor = "#FF0000",
downcolor = "#0000FF",
xlim = c(-3,3),
ylim = c(0,14))
Example with option 2 You can also specify the color of highlight.1 with upcolor parameter and highlight.2 with downcolor parameter.
<- plot_volcano(data = df,
volcano.result highlight.1 = c("ENSG00000169031.19","ENSG00000197385.5","ENSG00000111291.8"),
highlight.2 = c("ENSG00000123610.5","ENSG00000120217.14", "ENSG00000138646.9", "ENSG00000119922.10","ENSG00000185745.10"),
upcolor = "darkred",
downcolor = "darkblue",
xlim = c(-3,3),
ylim = c(0,14))
volcano.result
Saving figures
Figures can be saved using two approaches:
1. Using imbedded fucntion with predetermined dpi
plot_volcano(data = df,
geneset = dgs,
plot.save.to = "volcano_plot.png")
2. Using ggsave from the ggplot2 library with option to customize the width, height and dpi.
library(ggplot2)
ggsave("volcano_plot.png", volcano.result, width = 5, height = 5, dpi = 300)
This is the function to do pathway enrichment analysis (and visualization) with rWikiPathways (also KEGG, REACTOME & Hallmark) from a summary statistics table generated by differential expression analysis like limma or DESeq2. In directional enrichment analysis, the sign(positive/negative) indicates the direction of the enrichement, not the mathematical sign of -log10(FDR), for example, the positive sign indicate the up-regulated genes in geneset is over-represented in all the genes in the genome are up-regulated.
Below are the default parameters for plot_pathway. You can change
them to modify your output. Use help(plot_pathway)
to learn
more about the parameters.
plot_pathway(
data = df,
comp.names = NULL,
gene.id.type = "ENSEMBL",
FC.cutoff = 1.3,
FDR.cutoff = 0.05,
FCflag = "logFC",
FDRflag = "adj.P.Val",
Fisher.cutoff = 0.1,
Fisher.up.cutoff = 0.1,
Fisher.down.cutoff = 0.1,
plot.save.to = NULL,
pathway.db = "rWikiPathways"
)
Our sample dataset provided in the package only contains ENSEMBL gene
id types. Other types can be used by changing the parameter
gene.id.type = " id type"
. When inputing a single data
frame for analysis, comp.names
are not required. Currently
we are using rWikiPathways as a database for enrichment analysis but
this can be changed to KEGG, REACTOME, Hallmark or a static version of
rWikiPathways by changing the parameter
pathway.db = "database name"
.
<- plot_pathway(data = df, pathway.db = "Hallmark", gene.id.type = "ENSEMBL") pathway.result
1. Pathway analysis table with directional result (test up-regulated gene set and down-regulated gene set respectively).
head(pathway.result[[1]])
ID | Description | directional.p.adjust | direction | log10.padj | fil.cor |
---|---|---|---|---|---|
HALLMARK_INTERFERON_ALPHA_RESPONSE | HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.0000000 | down | -39.600163 | #1F78B4 |
HALLMARK_INFLAMMATORY_RESPONSE | HALLMARK_INFLAMMATORY_RESPONSE | 0.0000000 | down | -12.298898 | #1F78B4 |
HALLMARK_TNFA_SIGNALING_VIA_NFKB | HALLMARK_TNFA_SIGNALING_VIA_NFKB | 0.0000000 | down | -7.302635 | #1F78B4 |
HALLMARK_INTERFERON_GAMMA_RESPONSE | HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.0000000 | down | -52.486092 | #1F78B4 |
HALLMARK_COMPLEMENT | HALLMARK_COMPLEMENT | -0.0000473 | down | -4.325453 | #1F78B4 |
HALLMARK_IL6_JAK_STAT3_SIGNALING | HALLMARK_IL6_JAK_STAT3_SIGNALING | -0.0003144 | down | -3.502524 | #1F78B4 |
2. Pathway analysis table with non-directional fisher’s enrichment test result for all DE genes regardless of direction.
head(pathway.result[[2]])
ID | Description | pvalue | p.adjust |
---|---|---|---|
HALLMARK_INTERFERON_GAMMA_RESPONSE | HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.00e+00 | 0.0000000 |
HALLMARK_INTERFERON_ALPHA_RESPONSE | HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.00e+00 | 0.0000000 |
HALLMARK_INFLAMMATORY_RESPONSE | HALLMARK_INFLAMMATORY_RESPONSE | 0.00e+00 | 0.0000000 |
HALLMARK_TNFA_SIGNALING_VIA_NFKB | HALLMARK_TNFA_SIGNALING_VIA_NFKB | 1.00e-07 | 0.0000013 |
HALLMARK_COMPLEMENT | HALLMARK_COMPLEMENT | 1.92e-05 | 0.0001763 |
HALLMARK_IL6_JAK_STAT3_SIGNALING | HALLMARK_IL6_JAK_STAT3_SIGNALING | 4.26e-05 | 0.0003269 |
3. Pathway analysis plot with directional result.
3]] pathway.result[[
4. Pathway analysis plot with non-directional result.
4]] pathway.result[[
5. Pathway analysis plot with combined direaction and non-directional result.
5]] pathway.result[[
Saving figures
Figures can be saved using ggsave from the ggplot2 library.
library(ggplot2)
ggsave("joint_plot.png",pathway.result[[5]], width = 5, height = 5, dpi = 300)
Pathways with list of data as input, the list can be replaced with
d1
from the top. When list inputs are given
comp.names
should be speicified in order to identify the
comparison groups.
<- plot_pathway(data = list(df,df1),comp.names=c("A","B"),pathway.db = "Hallmark", gene.id.type = "ENSEMBL") list.pathway.result
1. Pathway analysis table with directional result for all datasets submited.
head(list.pathway.result[[1]])
Comparisons.ID | ID | Description | directional.p.adjust | direction | log10.padj | fil.cor |
---|---|---|---|---|---|---|
A | HALLMARK_INTERFERON_ALPHA_RESPONSE | HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.0000000 | down | -39.600163 | #1F78B4 |
A | HALLMARK_INFLAMMATORY_RESPONSE | HALLMARK_INFLAMMATORY_RESPONSE | 0.0000000 | down | -12.298898 | #1F78B4 |
A | HALLMARK_TNFA_SIGNALING_VIA_NFKB | HALLMARK_TNFA_SIGNALING_VIA_NFKB | 0.0000000 | down | -7.302635 | #1F78B4 |
A | HALLMARK_INTERFERON_GAMMA_RESPONSE | HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.0000000 | down | -52.486092 | #1F78B4 |
A | HALLMARK_COMPLEMENT | HALLMARK_COMPLEMENT | -0.0000473 | down | -4.325453 | #1F78B4 |
A | HALLMARK_IL6_JAK_STAT3_SIGNALING | HALLMARK_IL6_JAK_STAT3_SIGNALING | -0.0003144 | down | -3.502524 | #1F78B4 |
2. Pathway analysis table with non directional result for all datasets submited.
head(list.pathway.result[[2]])
Comparisons.ID | ID | Description | pvalue | p.adjust |
---|---|---|---|---|
A | HALLMARK_INTERFERON_GAMMA_RESPONSE | HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.00e+00 | 0.0000000 |
A | HALLMARK_INTERFERON_ALPHA_RESPONSE | HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.00e+00 | 0.0000000 |
A | HALLMARK_INFLAMMATORY_RESPONSE | HALLMARK_INFLAMMATORY_RESPONSE | 0.00e+00 | 0.0000000 |
A | HALLMARK_TNFA_SIGNALING_VIA_NFKB | HALLMARK_TNFA_SIGNALING_VIA_NFKB | 1.00e-07 | 0.0000013 |
A | HALLMARK_COMPLEMENT | HALLMARK_COMPLEMENT | 1.92e-05 | 0.0001763 |
A | HALLMARK_IL6_JAK_STAT3_SIGNALING | HALLMARK_IL6_JAK_STAT3_SIGNALING | 4.26e-05 | 0.0003269 |
3. Pathway analysis plot with directional result for list of summary tables.
3]] list.pathway.result[[
4. Pathway analysis plot with non directional result for list of summary tables.
4]] list.pathway.result[[
Saving figures
Figures can be saved using ggsave from the ggplot2 library.
library(ggplot2)
ggsave("non-directional.png",pathway.result[[4]], width = 5, height = 5, dpi = 300)
You can plot a heatmap from raw data rather than a summary statistics
table. plot_heatmap.expr
has the ability to calculate
average expression values and change from baseline. Importantly, these
calculations do not calculate statistical signifance or correct for
confounding factors - they should not be used as statistical analyses
but as data overviews.
For this, you need a count table and annotation table. The count
table should have the geneid as row names and the samples as column
names. These column names must match the sample.id
column
in your annotation file:
<- RVA::count_table[,1:50] count
1:6,1:5] count[
A1 | A10 | A11 | A12 | A13 | |
---|---|---|---|---|---|
ENSG00000121410.11 | 2 | 5 | 4 | 2 | 2 |
ENSG00000166535.19 | 0 | 0 | 0 | 0 | 0 |
ENSG00000094914.12 | 405 | 493 | 422 | 346 | 260 |
ENSG00000188984.11 | 0 | 0 | 0 | 0 | 0 |
ENSG00000204518.2 | 0 | 0 | 0 | 0 | 0 |
ENSG00000090861.15 | 555 | 782 | 674 | 435 | 268 |
<- RVA::sample_annotation[1:50,] annot
head(annot)
sample_id | tissue | subject_id | day | Treatment | subtissue |
---|---|---|---|---|---|
A1 | Blood | 1091 | 0 | Treatment_1 | Blood |
A10 | Blood | 1095 | 14 | Placebo | Blood |
A11 | Blood | 1095 | 28 | Placebo | Blood |
A12 | Blood | 1097 | 0 | Placebo | Blood |
A13 | Blood | 1097 | 14 | Placebo | Blood |
A14 | Blood | 1097 | 28 | Placebo | Blood |
Plot a simple summary of expression values:
Use help(plot_heatmap.expr)
for more information on the
parameters.
<- plot_heatmap.expr(data = count,
hm.expr annot = annot,
sample.id = "sample_id",
annot.flags = c("day", "Treatment"),
ct.table.id.type = "ENSEMBL",
gene.id.type = "SYMBOL",
gene.names = NULL,
gene.count = 10,
title = "RVA Heatmap",
fill = "CPM",
baseline.flag = "day",
baseline.val = "0",
plot.save.to = NULL,
input.type = "count")
The result of plot_heatmap.expr with fill = CPM contains 2 objects:
1. Heat map
2. A data frame of CPM values (fill = CPM in this example) for each geneid split by treatment group and time point.
head(hm.expr[[2]])
geneid | 0_Placebo | 0_Treatment_1 | 14_Placebo | 14_Treatment_1 | 28_Placebo | 28_Treatment_1 |
---|---|---|---|---|---|---|
ENSG00000019582 | 12.88519 | 12.95117 | 13.35188 | 13.10461 | 13.44575 | 12.92982 |
ENSG00000089157 | 13.53517 | 13.56759 | 13.09506 | 13.60246 | 13.16606 | 12.99473 |
ENSG00000142534 | 12.74876 | 12.79580 | 12.62589 | 12.97305 | 12.60354 | 12.21103 |
ENSG00000148303 | 12.96778 | 12.98249 | 12.68783 | 13.03604 | 12.77388 | 12.45019 |
ENSG00000156508 | 15.57407 | 15.63724 | 15.13047 | 15.42868 | 15.31821 | 15.33419 |
ENSG00000166710 | 13.69652 | 13.68064 | 14.08861 | 13.28912 | 14.16103 | 13.59287 |
Customize the plot & Save the figure
Here is an example of how you can customize your output dimensions and save your new output using the png() function. Always make sure that the ComplexHeatmap library is loaded for the draw function.
library(ComplexHeatmap)
png("heatmap_plots2cp.png", width = 500, height = 500)
draw(hm.expr$gp)
dev.off()
To calculate CFB from your input data, you must specify the baseline. The heatmap shown below compares each treatment on days 14 and 28 to the respective treatment on day 0.
Use help(plot_heatmap.expr)
for more information on the
parameters.
<- plot_heatmap.expr(data = count,
hm.expr.cfb annot = annot,
sample.id = "sample_id",
annot.flags = c("day", "Treatment"),
ct.table.id.type = "ENSEMBL",
gene.id.type = "SYMBOL",
gene.names = NULL,
gene.count = 10,
title = "RVA Heatmap",
fill = "CFB",
baseline.flag = "day",
baseline.val = "0",
plot.save.to = NULL,
input.type = "count")
The result of plot_heatmap.expr with fill = CFB contains 2 objects:
1. Heat map
2. A data frame of change from baselines values (fill = CFB in this example) for each geneid split by treatment group and time point.
head(hm.expr.cfb[[2]])
geneid | 14_Placebo | 14_Treatment_1 | 28_Placebo | 28_Treatment_1 |
---|---|---|---|---|
ENSG00000069482 | -3.120986 | 1.4161927 | -0.9142305 | 2.3416320 |
ENSG00000108107 | 2.930098 | -0.3906393 | 2.9803268 | -0.7834090 |
ENSG00000128422 | -2.060845 | 0.5122622 | -2.6034678 | 0.0996217 |
ENSG00000149925 | 2.735214 | -0.3762279 | 2.6791153 | -0.7753080 |
ENSG00000160862 | -2.688269 | 0.5648108 | -2.5291108 | 0.3503731 |
ENSG00000165953 | -3.160729 | 0.2600754 | -2.5078464 | 0.0210713 |
Customize the plot & Save the figure
Here is an example of how you can customize your output dimensions.
library(ComplexHeatmap)
png("heatmap_plots1cf.png", width = 500, height = 500)
draw(hm.expr.cfb$gp)
dev.off()
Let’s load in the sample data provided in this package. Note that the
count table containing data must have the geneid set as the rownames and
must have column names which match the sample.id
column of
the annotation file.
<- RVA::sample_annotation anno
head(anno)
sample_id | tissue | subject_id | day | Treatment | subtissue |
---|---|---|---|---|---|
A1 | Blood | 1091 | 0 | Treatment_1 | Blood |
A10 | Blood | 1095 | 14 | Placebo | Blood |
A11 | Blood | 1095 | 28 | Placebo | Blood |
A12 | Blood | 1097 | 0 | Placebo | Blood |
A13 | Blood | 1097 | 14 | Placebo | Blood |
A14 | Blood | 1097 | 28 | Placebo | Blood |
<- RVA::sample_count_cpm ct
1:6,1:5] ct[
A1 | A10 | A11 | A12 | A13 | |
---|---|---|---|---|---|
ENSG00000166535.19 | 8.5629 | 7.6227 | 7.7743 | 7.6845 | 8.5539 |
ENSG00000094914.12 | 3.1405 | 8.2261 | 7.9616 | 8.1047 | 7.8747 |
ENSG00000188984.11 | 5.7477 | 7.7889 | 8.0268 | 7.8954 | 8.0294 |
ENSG00000090861.15 | 8.2753 | 8.1688 | 8.6159 | 7.3708 | 7.7271 |
NA | NA | NA | NA | NA | NA |
NA.1 | NA | NA | NA | NA | NA |
Below is a simple plot using the defaults. Further parameter changes
can allow you to change the log scaling, the input type to either cpm or
count, and the genes selected for plotting. The sample table we are
using already has data points as CPM, so we will use CPM as our
input.type
.
Use help(plot_gene)
for more information on the
parameters.
<- plot_gene(ct,
gene.result
anno,gene.names = c("AAAS", "A2ML1", "AADACL3", "AARS"),
ct.table.id.type = "ENSEMBL",
gene.id.type = "SYMBOL",
treatment = "Treatment",
sample.id = "sample_id",
time = "day",
log.option = TRUE,
plot.save.to = NULL,
input.type = "cpm")
The result of plot_gene contains 2 objects:
1. A gene expression plot that distinguishes log cpm gene expression for each geneid across the treatment groups and time points.
2. A table that shows gene expression values by gene id, treatment group and time point with both sample ids and gene symbols.
head(gene.result[[2]])
geneid | sample_id | exprs | Treatment | day | SYMBOL |
---|---|---|---|---|---|
ENSG00000166535 | A1 | 8.5629 | Treatment_1 | 0 | A2ML1 |
ENSG00000166535 | A10 | 7.6227 | Placebo | 14 | A2ML1 |
ENSG00000166535 | A11 | 7.7743 | Placebo | 28 | A2ML1 |
ENSG00000166535 | A12 | 7.6845 | Placebo | 0 | A2ML1 |
ENSG00000166535 | A13 | 8.5539 | Placebo | 14 | A2ML1 |
ENSG00000166535 | A14 | 7.9185 | Placebo | 28 | A2ML1 |
Customize the plot & Save the figure
Here is an example of how you can customize your output dimensions and save your new plot using the ggsave function. Always make sure that the ggplot2 library is loaded.
library(ggplot2)
ggsave(gene.result, "gene_plots1_4.png", device = "png", width = 100, height = 100, dpi = 200, limitsize = FALSE)